Methods and compositions for analyzing nucleic acid molecules utilizing sizing techniques

ABSTRACT

Tags and linkers specifically designed for a wide variety of nucleic acid reactions are disclosed, which are suitable for a wide variety of nucleic acid reactions wherein separation of nucleic acid molecules based upon size is required.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. patent applicationSer. No. 08/786,834, filed Jan. 22, 1997, now abandoned; whichapplication claims the benefit of provisional application No.60/014,536, filed Jan. 23, 1996, and of provisional application No.60/020,487, filed Jun. 4, 1996, all of which are incorporated byreference herein in their entirety.

TECHNICAL FIELD

The present invention relates generally to methods and compositions foranalyzing nucleic acid molecules, and more specifically to tags whichmay be utilized in a wide variety of nucleic acid reactions, whereinseparation of nucleic acid molecules based on size is required.

BACKGROUND OF THE INVENTION

Detection and analysis of nucleic acid molecules are among the mostimportant techniques in biology. Such techniques are at the heart ofmolecular biology and play a rapidly expanding role in the rest ofbiology.

Generally, one type of analysis of nucleic acid reactions involvesseparation of nucleic acid molecules based on length. For example, onewidely used technique, polymerase chain reaction (PCR) (see, U.S. Pat.Nos. 4,683,195, 4,683,202, and 4,800,159) has become a widely utilizedtechnique to both identify sequences present in a sample and tosynthesize DNA molecules for further manipulation.

Briefly, in PCR, DNA sequences are amplified by enzymatic reaction thatsynthesizes new DNA strands in either a geometric or linear fashion.Following amplification, the DNA sequences must be detected andidentified. Because of non-specific amplifications, which wouldotherwise confuse analysis, or the need for purity, the PCR reactionproducts are generally subjected to separation prior to detection.Separation based on the size (i.e., length) of the products yields themost useful information. The method giving the highest resolution ofnucleic acid molecules is electrophoretic separation. In this method,each individual PCR reaction is applied to an appropriate gel andsubjected to a voltage potential. The number of samples that can beprocessed is limited by the number of wells in the gel. On most gelapparatus, from approximately 10 to 64 samples can be separated in asingle gel. Thus, processing large numbers of samples is both labor andmaterial intensive.

Electrophoretic separation must be coupled with some detection system inorder to obtain data. Detection systems of nucleic acids commonly, andalmost exclusively, utilize an intercalating dye or radioactive label,and less frequently, a nonradioactive label. Intercalating dyes, such asethidium bromide, are simple to use. The dye is included in the gelmatrix during electrophoresis or, following electrophoresis, the gel issoaked in a dye-containing solution. The dye can be directly visualizedin some cases, but more often, and for ethidium bromide in particular,is excited by light (e.g., UV) to fluoresce. In spite of this apparentease of use, such dyes have some notable disadvantages. First, the dyesare insensitive and there must be a large mass amount of nucleic acidmolecules in order to visualize the products. Second, the dyes aretypically mutagenic or carcinogenic.

A more sensitive detection technique than dyes uses a radioactive (ornonradioactive) label. Typically, either a radiolabeled nucleotide or aradiolabeled primer is included in the PCR reaction. Followingseparation, the radiolabel is “visualized” by autoradiography. Althoughmore sensitive, the detection suffers from film limitations, such asreciprocity failure and non-linearity. These limitations can be overcomeby detecting the label by phosphor image analysis. However, radiolabelshave safety requirements, increasing resource utilization andnecessitating specialized equipment and personnel training. For suchreasons, the use of nonradioactive labels has been increasing inpopularity. In such systems, nucleotides contain a label, such as afluorophore, biotin or digoxin, which can be detected by an antibody orother molecule (e.g., other member of a ligand pair) that is labeledwith an enzyme reactive with a chromogenic substrate. These systems donot have the safety concerns as described above, but use components thatare often labile and may yield nonspecific reactions, resulting in highbackground (i.e., low signal-to-noise ratio).

The present invention provides novel compositions and methods which maybe utilized in a wide variety of nucleic acid reactions, and furtherprovides other related advantages.

SUMMARY OF THE INVENTION

Briefly stated, the present invention provides compositions and methodswhich may be utilized in a wide variety of ligand pair reactions whereinseparation of molecules of interest, such as nucleic acid molecules,based on size is required. Representative examples of methods which maybe enhanced given the disclosure provided herein include PCR,differential display, RNA fingerprinting, PCR-SSCP, oligo litationsassays, nuclease digestion methods (e.g., exo- and endo-nuclease basedassays), and dideoxy fingerprinting. The methods described herein may beutilized in a wide array of fields, including, for example, in thedevelopment of clinical or research-based diagnostics, the determinationof polymorphisms, and the development of genetic maps.

Within one aspect of the present invention, methods are provided fordetermining the identity of a nucleic acid molecule, comprising thesteps of (a) generating tagged nucleic acid molecules from one or moreselected target nucleic acid molecules, wherein a tag is correlativewith a particular nucleic acid fragment and detectable bynon-fluorescent spectrometry or potentiometry, (b) separating the taggedfragments by size, (c) cleaving the tags from the tagged fragments, and(d) detecting tags by non-fluorescent spectrometry or potentiometry, andtherefrom determining the identity of the nucleic acid molecules.

Within a related aspect of the invention, methods are provided fordetecting a selected nucleic acid molecule, comprising the steps of (a)combining tagged nucleic acid probes with target nucleic acid moleculesunder conditions and for a time sufficient to permit hybridization of atagged nucleic acid probe to a complementary selected target nucleicacid sequence, wherein a tagged nucleic acid probe is detectable bynon-fluorescent spectrometry or potentiometry, (b) altering the size ofhybridized tagged probes, unhybridized probes or target molecules, orthe probe:target hybrids, (c) separating the tagged probes by size, (d)cleaving tags from the tagged probes, and (e) detecting the tags bynon-fluorescent spectrometry or potentiometry, and therefrom detectingthe selected nucleic acid molecule.

Within further aspects methods are provided for genotyping a selectedorganism, comprising the steps of (a) generating tagged nucleic acidmolecules from a selected target molecule, wherein a tag is correlativewith a particular fragment and may be detected by non-fluorescentspectrometry or potentiometry, (b) separating the tagged molecules bysequential length, (c) cleaving the tag from the tagged molecule, and(d) detecting the tag by non-fluorescent spectrometry or potentiometry,and therefrom determining the genotype of the organism.

Within another aspect, methods are provided for genotyping a selectedorganism, comprising the steps of (a) combining a tagged nucleic acidmolecule with a selected target molecule under conditions and for a timesufficient to permit hybridization of the tagged molecule to the targetmolecule, wherein a tag is correlative with a particular fragment andmay be detected by non-fluorescent spectrometry or potentiometry, (b)separating the tagged fragments by sequential length, (c) cleaving thetag from the tagged fragment, and (d) detecting the tag bynon-fluorescent spectrometry or potentiometry, and therefrom determiningthe genotype of the organism.

Within the context of the present invention it should be understood that“biological samples” include not only samples obtained from livingorganisms (e.g., mammals, fish, bacteria, parasites, viruses, fungi andthe like) or from the environment (e.g., air, water or solid samples),but biological materials which may be artificially or syntheticallyproduced (e.g., phage libraries, organic molecule libraries, pools ofgenomic clones, cDNA clones, RNA clones, or the like). Representativeexamples of biological samples include biological fluids (e.g., blood,semen, cerebral spinal fluid, urine), biological cells (e.g., stemcells, B or T cells, liver cells, fibroblasts and the like), andbiological tissues. Finally, representative examples of organisms thatmay be genotyped include virtually any unicellular or multicellularorganism, such as warm-blooded animals, mammals or vertebrates (e.g.,humans, chimps, macaques, horses, cows, pigs, sheep, dogs, cats, ratsand mice, as well as cells from any of these), bacteria, parasites,viruses, fungi and plants.

Within various embodiments of the above-described methods, the nucleicacid probes and or molecules of the present invention may be generatedby, for example, a ligation, cleavage or extension (e.g., PCR) reaction.Within other related aspects the nucleic acid probes or molecules may betagged by non-3′ tagged oligonucleotide primers (e.g., 5′-taggedoligonucleotide primers) or dideoxynucleotide terminators.

Within other embodiments of the invention, 4, 5, 10, 15, 20, 25, 30, 35,40, 45, 50, 60 , 70, 80, 90, 100, 200, 250, 300, 350, 400, 450, orgreater than 500 different and unique tagged molecules may be utilizedwithin a given reaction simultaneously, wherein each tag is unique for aselected nucleic acid molecule or fragment, or probe, and may beseparately identified.

Within further embodiments of the invention, the tag(s) may be detectedby fluorometry, mass spectrometry, infrared spectrometry, ultravioletspectrometry, or, potentiostatic amperometry (e.g., utilizingcoulometric or amperometric detectors). Representative examples ofsuitable spectrometric techniques include time-of-flight massspectrometry, quadrupole mass spectrometry, magnetic sector massspectrometry and electric sector mass spectrometry. Specific embodimentsof such techniques include ion-trap mass spectrometry, electrosprayionization mass spectrometry, ion-spray mass spectrometry, liquidionization mass spectrometry, atmospheric pressure ionization massspectrometry, electron ionization mass spectrometry, fast atom bombardionization mass spectrometry, MALDI mass spectrometry, photo-ionizationtime-of-flight mass spectrometry, laser droplet mass spectrometry,MALDI-TOF mass spectrometry, APCI mass spectrometry, nano-spray massspectrometry, nebulised spray ionization mass spectrometry, chemicalionization mass spectrometry, resonance ionization mass spectrometry,secondary ionization mass spectrometry and thermospray massspectrometry.

Within yet other embodiments of the invention, the target molecules,hybridized tagged probes, unhybridized probes or target molecules,probe:target hybrids, or tagged nucleic acid probes or molecules may beseparated from other molecules utilizing methods which discriminatebetween the size of molecules (either actual linear size, orthree-dimensional size). Representative examples of such methods includegel electrophoresis, capillary electrophoresis, micro-channelelectrophoresis, HPLC, size exclusion chromatography, filtration,polyacrylamide gel electrophoresis, liquid chromatography, reverse sizeexclusion chromatography, ion-exchange chromatography, reverse phaseliquid chromatography, pulsed-field electrophoresis, field-inversionelectrophoresis, dialysis, and fluorescence-activated liquid dropletsorting. Alternatively, the target molecules, hybridized tagged probes,unhybridized probes or target molecules, probe:target hybrids, or taggednucleic acid probes or molecules may be bound to a solid support (e.g.,hollow fibers (Amicon Corporation, Danvers, Mass.), beads (Polysciences,Warrington, Pa.), magnetic beads (Robbin Scientific, Mountain View,Calif.), plates, dishes and flasks (Coming Glass Works, Coming, N.Y.),meshes (Becton Dickinson, Mountain View, Calif.), screens and solidfibers (see Edelman et al., U.S. Pat. No. 3,843,324; see also Kurodaetÿal., U.S. Pat. No. 4,416,777), membranes (Millipore Corp., Bedford,Mass.), and dipsticks). If the first or second member, or exposednucleic acids are bound to a solid support, within certain embodimentsof the invention the methods disclosed herein may further comprise thestep of washing the solid support of unbound material.

Within other embodiments, the tagged nucleic acid molecules or probesmay be cleaved by a methods such as chemical, oxidation, reduction,acid-labile, base labile, enzymatic, electrochemical, heat andphotolabile methods. Within further embodiments, the steps ofseparating, cleaving and detecting may be performed in a continuousmanner, for example, on a single device which may be automated.

Within certain embodiments of the invention, the size of the hybridizedtagged probes, unhybridized probes or target molecules, or probe:targethybrids are altered by a method selected from the group consisting ofpolymerase extension, ligation, exonuclease digestion, endonucleasedigestion, restriction enzyme digestion, site-specific recombinasedigestion, ligation, mismatch specific nuclease digestion,methylation-specific nuclease digestion, covalent attachment of probe totarget and hybridization.

The methods an compositions described herein may be utilized in a widevariety of applications, including for example, identifying PCRamplicons, RNA fingerprinting, differential display, single-strandconformation polymorphism detection, dideoxyfingerprinting, restrictionmaps and restriction fragment length polymorphisms, DNA fingerprinting,genotyping, mutation detection, oligonucleotide ligation assay, sequencespecific amplifications, for diagnostics, forensics, identification,developmental biology, biology, molecular medicine, toxicology, animalbreeding,

These and other aspects of the present invention will become evidentupon reference to the following detailed description and attacheddrawings. In addition, various references are set forth below whichdescribe in more detail certain procedures or compositions (e.g.,plasmids, etc.), and are therefore incorporated by reference in theirentirety.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A, 1B, and 1C depicts the flowchart for the synthesis ofpentafluorophenyl esters of chemically cleavable mass spectroscopy tags,to liberate tags with carboxyl amide termini.

FIGS. 2A, 2B, and 2C depicts the flowchart for the synthesis ofpentafluorophenyl esters of chemically cleavable mass spectroscopy tags,to liberate tags with carboxyl acid termini.

FIGS. 3A, 3B, and 3C; 4A, 4B, and 4C; 5A, 5B, and 5C;-6A, 6B, and 6C;and 8A, 8B, and 8C depict the flowchart for the synthesis oftetrafluorophenyl esters of a set of 36 photochemically cleavable massspectroscopy tags.

FIGS. 7A, 7B, and 7C depicts the flowchart for the synthesis of a set of36 amine-terminated photochemically cleavable mass spectroscopy tags.

FIG. 9 depicts the synthesis of 36 photochemically cleavable massspectroscopy tagged oligonucleotides made from the corresponding set of36 tetrafluorophenyl esters of photochemically cleavable massspectroscopy tag acids.

FIGS. 10A and 10B depicts the synthesis of 36 photochemically cleavablemass spectroscopy tagged oligonucleotides made from the correspondingset of 36 amine-terminated photochemically cleavable mass spectroscopytags.

FIG. 11 illustrates the simultaneous detection of multiple tags by massspectrometry.

FIG. 12 shows the mass spectrogram of the alpha-cyano matrix alone.

FIG. 13 depicts a modularly-constructed tagged nucleic acid fragment.

FIGS. 14A-14I show the separation of DNA fragments by HPLC using avariety of different buffer solutions.

FIG. 15 is a schematic representation of genetic fingerprinting anddifferential display systems in accordance with an exemplary embodimentof the present invention.

FIG. 16 is a schematic representation of genetic fingerprinting anddifferential display systems in accordance with an exemplary embodimentof the present invention.

FIG. 17 is a schematic representation of assay systems in accordancewith an exemplary embodiment of the present invention.

FIG. 18 is a schematic representation of assay systems in accordancewith an exemplary embodiment of the present invention.

FIGS. 19A and 19B illustrate the preparation of a cleavable tag of thepresent invention.

FIGS. 20A and 20B illustrate the preparation of a cleavable tag of thepresent invention.

FIG. 21 illustrates the preparation of an intermediate compound usefulin the preparation of a cleavable tag of the invention.

DETAILED DESCRIPTION OF THE INVENTION

As noted above, the present invention provides compositions and methodsfor analyzing nucleic acid molecules, wherein separation of nucleic acidmolecules based on size is required. The present methods permit thesimultaneous detection of molecules of interest, which include nucleicacids and fragments, proteins, peptides, etc.

Briefly stated, in one aspect the present invention provides compoundswherein a molecule of interest, or precursor thereto, is linked via alabile bond (or labile bonds) to a tag. Thus, compounds of the inventionmay be viewed as having the general formula:

T—L—X

wherein T is the tag component, L is the linker component that eitheris, or contains, a labile bond, and X is either the molecule of interest(MOI) component or a functional group component (L_(h)) through whichthe MOI may be joined to T—L. Compounds of the invention may thereforebe represented by the more specific general formulas:

T—L—MOI

and

T—L—L_(h)

For reasons described in detail below, sets of T—L—MOI compounds may bepurposely subjected to conditions that cause the labile bond(s) tobreak, thus releasing a tag moiety from the remainder of the compound.The tag moiety is then characterized by one or more analyticaltechniques, to thereby provide direct information about the structure ofthe tag moiety, and (most importantly) indirect information about theidentity of the corresponding MOI.

As a simple illustrative example of a representative compound of theinvention wherein L is a direct bond, reference is made to the followingstructure (i):

In structure (i), T is a nitrogen-containing polycyclic aromatic moietybonded to a carbonyl group, X is a MOI (and specifically a nucleic acidfragment terminating in an amine group), and L is the bond which formsan amide group. The amide bond is labile relative to the bonds in Tbecause, as recognized in the art, an amide bond may be chemicallycleaved (broken) by acid or base conditions which leave the bonds withinthe tag component unchanged. Thus, a tag moiety (i.e., the cleavageproduct that contains T) may be released as shown below:

However, the linker L may be more than merely a direct bond, as shown inthe following illustrative example, where reference is made to anotherrepresentative compound of the invention having the structure (ii) shownbelow:

It is well-known that compounds having an ortho-nitrobenzylamine moiety(see boxed atoms within structure (ii)) are photolytically unstable, inthat exposure of such compounds to actinic radiation of a specifiedwavelength will cause selective cleavage of the benzylamine bond (seebond denoted with heavy line in structure (ii)). Thus, structure (ii)has the same T and MOI groups as structure (i), however the linker groupcontains multiple atoms and bonds within which there is a particularlylabile bond. Photolysis of structure (ii) thus releases a tag moiety(T-containing moiety) from the remainder of the compound, as shownbelow.

The invention thus provides compounds which, upon exposure toappropriate cleavage conditions, undergo a cleavage reaction so as torelease a tag moiety from the remainder of the compound. Compounds ofthe invention may be described in terms of the tag moiety, the MOI (orprecursor thereto, L_(h)), and the labile bond(s) which join the twogroups together. Alternatively, the compounds of the invention may bedescribed in terms of the components from which they are formed. Thus,the compounds may be described as the reaction product of a tagreactant, a linker reactant and a MOI reactant, as follows.

The tag reactant consists of a chemical handle (T_(h)) and a variablecomponent (T_(vc)), so that the tag reactant is seen to have the generalstructure:

T_(vc)—T_(h)

To illustrate this nomenclature, reference may be made to structure(iii), which shows a tag reactant that may be used to prepare thecompound of structure (ii). The tag reactant having structure (iii)contains a tag variable component and a tag handle, as shown below:

In structure (iii), the tag handle (—C(═O)—A) simply provides an avenuefor reacting the tag reactant with the linker reactant to form a T—Lmoiety. The group “A” in structure (iii) indicates that the carboxylgroup is in a chemically active state, so it is ready for coupling withother handles. “A” may be, for example, a hydroxyl group orpentafluorophenoxy, among many other possibilities. The inventionprovides for a large number of possible tag handles which may be bondedto a tag variable component, as discussed in detail below. The tagvariable component is thus a part of “T” in the formula T—L—X, and willalso be part of the tag moiety that forms from the reaction that cleavesL.

As also discussed in detail below, the tag variable component isso-named because, in preparing sets of compounds according to theinvention, it is desired that members of a set have unique variablecomponents, so that the individual members may be distinguished from oneanother by an analytical technique. As one example, the tag variablecomponent of structure (iii) may be one member of the following set,where members of the set may be distinguished by their UV or massspectra:

Likewise, the linker reactant may be described in terms of its chemicalhandles (there are necessarily at least two, each of which may bedesignated as L_(h)) which flank a linker labile component, where thelinker labile component consists of the required labile moiety (L²) andoptional labile moieties (L¹ and L³), where the optional labile moietieseffectively serve to separate L² from the handles L_(h), and therequired labile moiety serves to provide a labile bond within the linkerlabile component. Thus, the linker reactant may be seen to have thegeneral formula:

L_(h)—L¹—L²—L³—L_(h)

The nomenclature used to describe the linker reactant may be illustratedin view of structure (iv), which again draws from the compound ofstructure (ii):

As structure (iv) illustrates, atoms may serve in more than onefunctional role. Thus, in structure (iv), the benzyl nitrogen functionsas a chemical handle in allowing the linker reactant to join to the tagreactant via an amide-forming reaction, and subsequently also serves asa necessary part of the structure of the labile moiety L² in that thebenzylic carbon-nitrogen bond is particularly susceptible to photolyticcleavage. Structure (iv) also illustrates that a linker reactant mayhave an L³ group (in this case, a methylene group), although not have anL¹ group. Likewise, linker reactants may have an L¹ group but not an L³group, or may have L¹ and L³ groups, or may have neither of L¹ nor L³groups. In structure (iv), the presence of the group “P” next to thecarbonyl group indicates that the carbonyl group is protected fromreaction. Given this configuration, the activated carboxyl group of thetag reactant (iii) may cleanly react with the amine group of the linkerreactant (iv) to form an amide bond and give a compound of the formulaT—L—L_(h).

The MOI reactant is a suitably reactive form of a molecule of interest.Where the molecule of interest is a nucleic acid fragment, a suitableMOI reactant is a nucleic acid fragment bonded through its 5′ hydroxylgroup to a phosphodiester group and then to an alkylene chain thatterminates in an amino group. This amino group may then react with thecarbonyl group of structure (iv), (after, of course, deprotecting thecarbonyl group, and preferably after subsequently activating thecarbonyl group toward reaction with the amine group) to thereby join theMOI to the linker.

When viewed in a chronological order, the invention is seen to take atag reactant (having a chemical tag handle and a tag variablecomponent), a linker reactant (having two chemical linker handles, arequired labile moiety and 0-2 optional labile moieties) and a MOIreactant (having a molecule of interest component and a chemicalmolecule of interest handle) to form T—L—MOI. Thus, to form T—L—MOI,either the tag reactant and the linker reactant are first reactedtogether to provide T—L—L_(h), and then the MOI reactant is reacted withT—L—L_(h) so as to provide T—L—MOI, or else (less preferably) the linkerreactant and the MOI reactant are reacted together first to provideL_(h)—L—MOI, and then L_(h)—L—MOI is reacted with the tag reactant toprovide T—L—MOI. For purposes of convenience, compounds having theformula T—L—MOI will be described in terms of the tag reactant, thelinker reactant and the MOI reactant which may be used to form suchcompounds. Of course, the same compounds of formula T—L—MOI could beprepared by other (typically, more laborious) methods, and still fallwithin the scope of the inventive T—L—MOI compounds.

In any event, the invention provides that a T—L—MOI compound besubjected to cleavage conditions, such that a tag moiety is releasedfrom the remainder of the compound. The tag moiety will comprise atleast the tag variable component, and will typically additionallycomprise some or all of the atoms from the tag handle, some or all ofthe atoms from the linker handle that was used to join the tag reactantto the linker reactant, the optional labile moiety L¹ if this group waspresent in T—L—MOI, and will perhaps contain some part of the requiredlabile moiety L² depending on the precise structure of L² and the natureof the cleavage chemistry. For convenience, the tag moiety may bereferred to as the T-containing moiety because T will typicallyconstitute the major portion (in terms of mass) of the tag moiety.

Given this introduction to one aspect of the present invention, thevarious components T, L and X will be described in detail. Thisdescription begins with the following definitions of certain terms,which will be used hereinafter in describing T, L and X.

As used herein, the term “nucleic acid fragment” means a molecule whichis complementary to a selected target nucleic acid molecule (i.e.,complementary to all or a portion thereof), and may be derived fromnature or synthetically or recombinantly produced, includingnon-naturally occurring molecules, and may be in double or singlestranded form where appropriate; and includes an oligonucleotide (e.g.,DNA or RNA), a primer, a probe, a nucleic acid analog (e.g., PNA), anoligonucleotide which is extended in a 5′ to 3′ direction by apolymerase, a nucleic acid which is cleaved chemically or enzymatically,a nucleic acid that is terminated with a dideoxy terminator or capped atthe 3′ or 5′ end with a compound that prevents polymerization at the 5′or 3′ end, and combinations thereof. The complementarity of a nucleicacid fragment to a selected target nucleic acid molecule generally meansthe exhibition of at least about 70% specific base pairing throughoutthe length of the fragment. Preferably the nucleic acid fragmentexhibits at least about 80% specific base pairing; and most preferablyat least about 90%. Assays for determining the percent mismatch (andthus the percent specific base pairing) are well known in the art andare based upon the percent mismatch as a function of the Tm whenreferenced to the fully base paired control.

As used herein, the term “alkyl,” alone or in combination, refers to asaturated, straight-chain or branched-chain hydrocarbon radicalcontaining from 1 to 10, preferably from 1 to 6 and more preferably from1 to 4, carbon atoms. Examples of such radicals include, but are notlimited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, iso-butyl,sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl, decyl and the like. Theterm “alkylene” refers to a saturated, straight-chain or branched chainhydrocarbon diradical containing from 1 to 10, preferably from 1 to 6and more preferably from 1 to 4, carbon atoms. Examples of suchdiradicals include, but are not limited to, methylene, ethylene(—CH₂—CH₂—), propylene, and the like.

The term “alkenyl,” alone or in combination, refers to a straight-chainor branched-chain hydrocarbon radical having at least one carbon-carbondouble bond in a total of from 2 to 10, preferably from 2 to 6 and morepreferably from 2 to 4, carbon atoms. Examples of such radicals include,but are not limited to, ethenyl, E- and Z-propenyl, isopropenyl, E- andZ-butenyl, E- and Z-isobutenyl, E- and Z-pentenyl, decenyl and the like.The term “alkenylene” refers to a straight-chain or branched-chainhydrocarbon diradical having at least one carbon-carbon double bond in atotal of from 2 to 10, preferably from 2 to 6 and more preferably from 2to 4, carbon atoms. Examples of such diradicals include, but are notlimited to, methylidene (═CH₂), ethylidene (—CH═CH—), propylidene(—CH₂—CH═CH—) and the like.

The term “alkynyl,” alone or in combination, refers to a straight-chainor branched-chain hydrocarbon radical having at least one carbon-carbontriple bond in a total of from 2 to 10, preferably from 2 to 6 and morepreferably from 2 to 4, carbon atoms. Examples of such radicals include,but are not limited to, ethynyl (acetylenyl), propynyl (propargyl),butynyl, hexynyl, decynyl and the like. The term “alkynylene”, alone orin combination, refers to a straight-chain or branched-chain hydrocarbondiradical having at least one carbon-carbon triple bond in a total offrom 2 to 10, preferably from 2 to 6 and more preferably from 2 to 4.carbon atoms. Examples of such radicals include, but are not limited,ethynylene (—C≡C—), propynylene (—CH₂—C≡C—) and the like.

The term “cycloalkyl,” alone or in combination, refers to a saturated,cyclic arrangement of carbon atoms which number from 3 to 8 andpreferably from 3 to 6, carbon atoms. Examples of such cycloalkylradicals include, but are not limited to, cyclopropyl, cyclobutyl,cyclopentyl, cyclohexyl and the like. The term “cycloalkylene” refers toa diradical form of a cycloalkyl.

The term “cycloalkenyl,” alone or in combination, refers to a cycliccarbocycle containing from 4 to 8, preferably 5 or 6, carbon atoms andone or more double bonds. Examples of such cycloalkenyl radicalsinclude, but are not limited to, cyclopentenyl, cyclohexenyl,cyclopentadienyl and the like. The term “cycloalkenylene” refers to adiradical form of a cycloalkenyl.

The term “aryl” refers to a carbocyclic (consisting entirely of carbonand hydrogen) aromatic group selected from the group consisting ofphenyl, naphthyl, indenyl, indanyl, azulenyl, fluorenyl, andanthracenyl; or a heterocyclic aromatic group selected from the groupconsisting of furyl, thienyl, pyridyl, pyrrolyl, oxazolyly, thiazolyl,imidazolyl, pyrazolyl, 2-pyrazolinyl, pyrazolidinyl, isoxazolyl,isothiazolyl, 1,2,3-oxadiazolyl, 1,2,3-triazolyl, 1,3,4-thiadiazolyl,pyridazinyl, pyrimidinyl, pyrazinyl, 1,3,5-triazinyl, 1,3,5-trithianyl,indolizinyl, indolyl, isoindolyl, 3H-indolyl, indolinyl,benzo[b]furanyl, 2,3-dihydrobenzofuranyl, benzo[b]thiophenyl,1H-indazolyl, benzimidazolyl, benzthiazolyl, purinyl, 4H-quinolizinyl,quinolinyl, isoquinolinyl, cinnolinyl, phthalazinyl, quinazolinyl,quinoxalinyl, 1,8-naphthyridinyl, pteridinyl, carbazolyl, acridinyl,phenazinyl, phenothiazinyl, and phenoxazinyl.

“Aryl” groups, as defined in this application may independently containone to four substituents which are independently selected from the groupconsisting of hydrogen, halogen, hydroxyl, amino, nitro,trifluoromethyl, trifluoromethoxy, alkyl, alkenyl, alkynyl, cyano,carboxy, carboalkoxy, 1,2-dioxyethylene, alkoxy, alkenoxy or alkynoxy,alkylamino, alkenylamino, alkynylamino, aliphatic or aromatic acyl,alkoxy-carbonylamino, alkylsulfonylamino, morpholinocarbonylamino,thiomorpholinocarbonylamino, N-alkyl guanidino, aralkylaminosulfonyl;aralkoxyalkyl; N-aralkoxyurea; N-hydroxylurea; N-alkenylurea;N,N-(alkyl, hydroxyl)urea; heterocyclyl; thioaryloxy-substituted aryl;N,N-(aryl, alkyl)hydrazino; Ar′-substituted sulfonylheterocyclyl;aralkyl-substituted heterocyclyl; cycloalkyl and cycloakenyl-substitutedheterocyclyl; cycloalkyl-fused aryl; aryloxy-substituted alkyl;heterocyclylamino; aliphatic or aromatic acylaminocarbonyl; aliphatic oraromatic acyl-substituted alkenyl; Ar′-substituted aminocarbonyloxy;Ar′, Ar′-disubstituted aryl; aliphatic or aromatic acyl-substitutedacyl; cycloalkylcarbonylalkyl; cycloalkyl-substituted amino;aryloxycarbonylalkyl; phosphorodiamidyl acid or ester;

“Ar′” is a carbocyclic or heterocyclic aryl group as defined abovehaving one to three substituents selected from the group consisting ofhydrogen, halogen, hydroxyl, amino, nitro, trifluoromethyl,trifluoromethoxy, alkyl, alkenyl, alkynyl, 1,2-dioxymethylene,1,2-dioxyethylene, alkoxy, alkenoxy, alkynoxy, alkylamino, alkenylaminoor alkynylamino, alkylcarbonyloxy, aliphatic or aromatic acyl,alkylcarbonylamino, alkoxycarbonylamino, alkylsulfonylamino, N-alkyl orN,N-dialkyl urea.

The term “alkoxy,” alone or in combination, refers to an alkyl etherradical, wherein the term “alkyl” is as defined above. Examples ofsuitable alkyl ether radicals include, but are not limited to, methoxy,ethoxy, n-propoxy, iso-propoxy, n-butoxy, iso-butoxy, sec-butoxy,tert-butoxy and the like.

The term “alkenoxy,” alone or in combination, refers to a radical offormula alkenyl-O—, wherein the term “alkenyl” is as defined aboveprovided that the radical is not an enol ether. Examples of suitablealkenoxy radicals include, but are not limited to, allyloxy, E- andZ-3-methyl-2-propenoxy and the like.

The term “alkynyloxy,” alone or in combination, refers to a radical offormula alkynyl-O—, wherein the term “alkynyl” is as defined aboveprovided that the radical is not an ynol ether. Examples of suitablealkynoxy radicals include, but are not limited to, propargyloxy,2-butynyloxy and the like.

The term “thioalkoxy” refers to a thioether radical of formula alkyl-S—,wherein alkyl is as defined above.

The term “alkylamino,” alone or in combination, refers to a mono- ordi-alkyl-substituted amino radical (i.e., a radical of formula alkyl-NH—or (alkyl)₂-N—), wherein the term “alkyl” is as defined above. Examplesof suitable alkylamino radicals include, but are not limited to,methylamino, ethylamino, propylamino, isopropylamino, t-butylamino,N,N-diethylamino and the like.

The term “alkenylamino,” alone or in combination, refers to a radical offormula alkenyl-NH— or (alkenyl)₂N—, wherein the term “alkenyl” is asdefined above, provided that the radical is not an enamine. An exampleof such alkenylamino radicals is the allylamino radical.

The term “alkynylamino,” alone or in combination, refers to a radical offormula alkynyl-NH— or (alkynyl)₂N—, wherein the term “alkynyl” is asdefined above, provided that the radical is not an ynamine. An exampleof such alkynylamino radicals is the propargyl amino radical.

The term “amide” refers to either —N(R¹)—C(═O)— or —C(═O)—N(R¹)— whereR¹ is defined herein to include hydrogen as well as other groups. Theterm “substituted amide” refers to the situation where R¹ is nothydrogen, while the term “unsubstituted amide” refers to the situationwhere R¹ is hydrogen.

The term “aryloxy,” alone or in combination, refers to a radical offormula aryl-O—, wherein aryl is as defined above. Examples of aryloxyradicals include, but are not limited to, phenoxy, naphthoxy, pyridyloxyand the like.

The term “arylamino,” alone or in combination, refers to a radical offormula aryl-NH—, wherein aryl is as defined above. Examples ofarylamino radicals include, but are not limited to, phenylamino(anilido), naphthylamino, 2-, 3- and 4-pyridylamino and the like.

The term “aryl-fused cycloalkyl,” alone or in combination, refers to acycloalkyl radical which shares two adjacent atoms with an aryl radical,wherein the terms “cycloalkyl” and “aryl” are as defined above. Anexample of an aryl-fused cycloalkyl radical is the benzofused cyclobutylradical.

The term “alkylcarbonylamino,” alone or in combination, refers to aradical of formula alkyl-CONH, wherein the term “alkyl” is as definedabove.

The term “alkoxycarbonylamino,” alone or in combination, refers to aradical of formula alkyl-OCONH—, wherein the term “alkyl” is as definedabove.

The term “alkylsulfonylamino,” alone or in combination, refers to aradical of formula alkyl-SO₂NH—, wherein the term “alkyl” is as definedabove.

The term “arylsulfonylamino,” alone or in combination, refers to aradical of formula aryl-SO₂NH—, wherein the term “aryl” is as definedabove.

The term “N-alkylurea,” alone or in combination, refers to a radical offormula alkyl-NH—CO—NH—, wherein the term “alkyl” is as defined above.

The term “N-arylurea,” alone or in combination, refers to a radical offormula aryl-NH—CO—NH—, wherein the term “aryl” is as defined above.

The term “halogen” means fluorine, chlorine, bromine and iodine.

The term “hydrocarbon radical” refers to an arrangement of carbon andhydrogen atoms which need only a single hydrogen atom to be anindependent stable molecule. Thus, a hydrocarbon radical has one openvalence site on a carbon atom, through which the hydrocarbon radical maybe bonded to other atom(s). Alkyl, alkenyl, cycloalkyl, etc. areexamples of hydrocarbon radicals.

The term “hydrocarbon diradical” refers to an arrangement of carbon andhydrogen atoms which need two hydrogen atoms in order to be anindependent stable molecule. Thus, a hydrocarbon radical has two openvalence sites on one or two carbon atoms, through which the hydrocarbonradical may be bonded to other atom(s). Alkylene, alkenylene,alkynylene, cycloalkylene, etc. are examples of hydrocarbon diradicals.

The term “hydrocarbyl” refers to any stable arrangement consistingentirely of carbon and hydrogen having a single valence site to which itis bonded to another moiety, and thus includes radicals known as alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl (without heteroatomincorporation into the aryl ring), arylalkyl, alkylaryl and the like.Hydrocarbon radical is another name for hydrocarbyl.

The term “hydrocarbylene” refers to any stable arrangement consistingentirely of carbon and hydrogen having two valence sites to which it isbonded to other moieties, and thus includes alkylene, alkenylene,alkynylene, cycloalkylene, cycloalkenylene, arylene (without heteroatomincorporation into the arylene ring), arylalkylene, alkylarylene and thelike. Hydrocarbon diradical is another name for hydrocarbylene.

The term “hydrocarbyl-O-hydrocarbylene” refers to a hydrocarbyl groupbonded to an oxygen atom, where the oxygen atom is likewise bonded to ahydrocarbylene group at one of the two valence sites at which thehydrocarbylene group is bonded to other moieties. The terms“hydrocarbyl-S-hydrocarbylene”, “hydrocarbyl-NH-hydrocarbylene” and“hydrocarbyl-amide-hydrocarbylene” have equivalent meanings, whereoxygen has been replaced with sulfur, —NH— or an amide group,respectively.

The term N-(hydrocarbyl)hydrocarbylene refers to a hydrocarbylene groupwherein one of the two valence sites is bonded to a nitrogen atom, andthat nitrogen atom is simultaneously bonded to a hydrogen and ahydrocarbyl group. The term N,N-di(hydrocarbyl)hydrocarbylene refers toa hydrocarbylene group wherein one of the two valence sites is bonded toa nitrogen atom, and that nitrogen atom is simultaneously bonded to twohydrocarbyl groups.

The term “hydrocarbylacyl-hydrocarbylene” refers to a hydrocarbyl groupbonded through an acyl (—C(═O)—) group to one of the two valence sitesof a hydrocarbylene group.

The terms “heterocyclylhydrocarbyl” and “heterocylyl” refer to a stable,cyclic arrangement of atoms which include carbon atoms and up to fouratoms (referred to as heteroatoms) selected from oxygen, nitrogen,phosphorus and sulfur. The cyclic arrangement may be in the form of amonocyclic ring of 3-7 atoms, or a bicyclic ring of 8-11 atoms. Therings may be saturated or unsaturated (including aromatic rings), andmay optionally be benzofused. Nitrogen and sulfur atoms in the ring maybe in any oxidized form, including the quaternized form of nitrogen. Aheterocyclylhydrocarbyl may be attached at any endocyclic carbon orheteroatom which results in the creation of a stable structure.Preferred heterocyclylhydrocarbyls include 5-7 membered monocyclicheterocycles containing one or two nitrogen heteroatoms.

A substituted heterocyclylhydrocarbyl refers to aheterocyclylhydrocarbyl as defined above, wherein at least one ring atomthereof is bonded to an indicated substituent which extends off of thering.

In referring to hydrocarbyl and hydrocarbylene groups, the term“derivatives of any of the foregoing wherein one or more hydrogens isreplaced with an equal number of fluorides” refers to molecules thatcontain carbon, hydrogen and fluoride atoms, but no other atoms.

The term “activated ester” is an ester that contains a “leaving group”which is readily displaceable by a nucleophile, such as an amine, andalcohol or a thiol nucleophile. Such leaving groups are well known andinclude, without limitation, N-hydroxysuccinimide,N-hydroxybenzotriazole, halogen (halides), alkoxy includingtetrafluorophenolates, thioalkoxy and the like. The term “protectedester” refers to an ester group that is masked or otherwise unreactive.See, e.g., Greene, “Protecting Groups In Organic Synthesis.”

In view of the above definitions, other chemical terms used throughoutthis application can be easily understood by those of skill in the art.Terms may be used alone or in any combination thereof. The preferred andmore preferred chain lengths of the radicals apply to all suchcombinations.

A. Generation of Tagged Nucleic Acid Fragments

As noted above, one aspect of the present invention provides a generalscheme for DNA sequencing which allows the use of more than 16 tags ineach lane; with continuous detection, the tags can be detected and thesequence read as the size separation is occurring, just as withconventional fluorescence-based sequencing. This scheme is applicable toany of the DNA sequencing techniques-based on size separation of taggedmolecules. Suitable tags and linkers for use within the presentinvention, as well as methods for sequencing nucleic acids, arediscussed in more detail below.

1. Tags

“Tag”, as used herein, generally refers to a chemical moiety which isused to uniquely identify a “molecule of interest”, and morespecifically refers to the tag variable component as well as whatevermay be bonded most closely to it in any of the tag reactant, tagcomponent and tag moiety.

A tag which is useful in the present invention possesses severalattributes:

1) It is capable of being distinguished from all other tags. Thisdiscrimination from other chemical moieties can be based on thechromatographic behavior of the tag (particularly after the cleavagereaction), its spectroscopic or potentiometric properties, or somecombination thereof. Spectroscopic methods by which tags are usefullydistinguished include mass spectroscopy (MS), infrared (IR), ultraviolet(UV), and fluorescence, where MS, IR and UV are preferred, and MS mostpreferred spectroscopic methods. Potentiometric amperometry is apreferred potentiometric method.

2) The tag is capable of being detected when present at 10⁻²² to 10⁻⁶mole.

3) The tag possesses a chemical handle through which it can be attachedto the MOI which the tag is intended to uniquely identify. Theattachment may be made directly to the MOI, or indirectly through a“linker” group.

4) The tag is chemically stable toward all manipulations to which it issubjected, including attachment and cleavage from the MOI, and anymanipulations of the MOI while the tag is attached to it.

5) The tag does not significantly interfere with the manipulationsperformed on the MOI while the tag is attached to it. For instance, ifthe tag is attached to an oligonucleotide, the tag must notsignificantly interfere with any hybridization or enzymatic reactions(e.g., PCR sequencing reactions) performed on the oligonucleotide.Similarly, if the tag is attached to an antibody, it must notsignificantly interfere with antigen recognition by the antibody.

A tag moiety which is intended to be detected by a certain spectroscopicor potentiometric method should possess properties which enhance thesensitivity and specificity of detection by that method. Typically, thetag moiety will have those properties because they have been designedinto the tag variable component, which will typically constitute themajor portion of the tag moiety. In the following discussion, the use ofthe word “tag” typically refers to the tag moiety (i.e., the cleavageproduct that contains the tag variable component), however can also beconsidered to refer to the tag variable component itself because that isthe portion of the tag moiety which is typically responsible forproviding the uniquely detectable properties. In compounds of theformula T—L—X, the “T” portion will contain the tag variable component.Where the tag variable component has been designed to be characterizedby, e.g., mass spectrometry, the “T” portion of T—L—X may be referred toas T^(ms). Likewise, the cleavage product from T—L—X that contains T maybe referred to as the T^(ms)-containing moiety. The followingspectroscopic and potentiometric methods may be used to characterizeT^(ms)-containing moieties.

a. Characteristics of MS Tags

Where a tag is analyzable by mass spectrometry (i.e., is a MS-readabletag, also referred to herein as a MS tag or “T^(ms)-containing moiety”),the essential feature of the tag is that it is able to be ionized. It isthus a preferred element in the design of MS-readable tags toincorporate therein a chemical functionality which can carry a positiveor negative charge under conditions of ionization in the MS. Thisfeature confers improved efficiency of ion formation and greater overallsensitivity of detection, particularly in electrospray ionization. Thechemical functionality that supports an ionized charge may derive fromT^(ms) or L or both. Factors that can increase the relative sensitivityof an analyte being detected by mass spectrometry are discussed in,e.g., Sunner, J., et al., Anal. Chem. 60:1300-1307 (1988).

A preferred functionality to facilitate the carrying of a negativecharge is an organic acid, such as phenolic hydroxyl, carboxylic acid,phosphonate, phosphate, tetrazole, sulfonyl urea, perfluoro alcohol andsulfonic acid.

Preferred functionality to facilitate the carrying of a positive chargeunder ionization conditions are aliphatic or aromatic amines. Examplesof amine functional groups which give enhanced detectability of MS tagsinclude quaternary amines (i.e., amines that have four bonds, each tocarbon atoms, see Aebersold, U.S. Pat. No. 5,240,859) and tertiaryamines (i.e., amines that have three bonds, each to carbon atoms, whichincludes C═N—C groups such as are present in pyridine, see Hess et al.,Anal. Biochem. 224:373, 1995; Bures et al., Anal. Biochem. 224:364,1995). Hindered tertiary amines are particularly preferred. Tertiary andquaternary amines may be alkyl or aryl. A T^(ms)-containing moiety mustbear at least one ionizable species, but may possess more than oneionizable species. The preferred charge state is a single ionizedspecies per tag. Accordingly, it is preferred that eachT^(ms)-containing moiety (and each tag variable component) contain onlya single hindered amine or organic acid group.

Suitable amine-containing radicals that may form part of theT^(ms)-containing moiety include the following:

The identification of a tag by mass spectrometry is preferably basedupon its molecular mass to charge ratio (m/z). The preferred molecularmass range of MS tags is from about 100 to 2,000 daltons, and preferablythe T^(ms)-containing moiety has a mass of at least about 250 daltons,more preferably at least about 300 daltons, and still more preferably atleast about 350 daltons. It is generally difficult for massspectrometers to distinguish among moieties having parent ions belowabout 200-250 daltons (depending on the precise instrument), and thuspreferred T^(ms)-containing moieties of the invention have masses abovethat range.

As explained above, the T^(ms)-containing moiety may contain atoms otherthan those present in the tag variable component, and indeed other thanpresent in T^(ms) itself. Accordingly, the mass of T^(ms) itself may beless than about 250 daltons, so long as the T^(ms)-containing moiety hasa mass of at least about 250 daltons. Thus, the mass of T^(ms) may rangefrom 15 (i.e., a methyl radical) to about 10,000 daltons, and preferablyranges from 100 to about 5,000 daltons, and more preferably ranges fromabout 200 to about 1,000 daltons.

It is relatively difficult to distinguish tags by mass spectrometry whenthose tags incorporate atoms that have more than one isotope insignificant abundance. Accordingly, preferred T groups which areintended for mass spectroscopic identification (T^(ms) groups), containcarbon, at least one of hydrogen and fluoride, and optional atomsselected from oxygen, nitrogen, sulfur, phosphorus and iodine. Whileother atoms may be present in the T^(ms), their presence can renderanalysis of the mass spectral data somewhat more difficult. Preferably,the T^(ms) groups have only carbon, nitrogen and oxygen atoms, inaddition to hydrogen and/or fluoride.

Fluoride is an optional yet preferred atom to have in a T^(ms) group. Incomparison to hydrogen, fluoride is, of course, much heavier. Thus, thepresence of fluoride atoms rather than hydrogen atoms leads to T^(ms)groups of higher mass, thereby allowing the T^(ms) group to reach andexceed a mass of greater than 250 daltons, which is desirable asexplained above. In addition, the replacement of hydrogen with fluorideconfers greater volatility on the T^(ms)-containing moiety, and greatervolatility of the analyte enhances sensitivity when mass spectrometry isbeing used as the detection method.

The molecular formula of T^(ms) falls within the scope ofC₁₋₅₀₀N₀₋₁₀₀O₀₋₁₀₀S₀₋₁₀P₀₋₁₀H_(α)F_(β)I_(δ) wherein the sum of α, β andδ is sufficient to satisfy the otherwise unsatisfied valencies of the C,N, O, S and P atoms. The designationC₁₋₅₀₀N₀₋₁₀₀O₀₋₁₀₀S₀₋₁₀P₀₋₁₀H_(α)F_(β)I_(δ) means that T^(ms) containsat least one, and may contain any number from 1 to 500 carbon atoms, inaddition to optionally containing as many as 100 nitrogen atoms (“N₀₋”means that T^(ms) need not contain any nitrogen atoms), and as many as100 oxygen atoms, and as many as 10 sulfur atoms and as many as 10phosphorus atoms. The symbols α, β and δ represent the number ofhydrogen, fluoride and iodide atoms in T^(ms), where any two of thesenumbers may be zero, and where the sum of these numbers equals the totalof the otherwise unsatisfied valencies of the C, N, O, S and P atoms.Preferably, T^(ms) has a molecular formula that falls within the scopeof C₁₋₅₀N₀₋₁₀O₀₋₁₀H_(α)F_(β) where the sum of α and β equals the numberof hydrogen and fluoride atoms, respectively, present in the moiety.

b. Characteristics of IR Tags

There are two primary forms of IR detection of organic chemical groups:Raman scattering IR and absorption IR. Raman scattering IR spectra andabsorption IR spectra are complementary spectroscopic methods. Ingeneral, Raman excitation depends on bond polarizability changes whereasIR absorption depends on bond dipole moment changes. Weak IR absorptionlines become strong Raman lines and vice versa. Wavenumber is thecharacteristic unit for IR spectra. There are 3 spectral regions for IRtags which have separate applications: near IR at 12500 to 4000 cm⁻¹,mid IR at 4000 to 600 cm⁻¹, far IR at 600 to 30 cm⁻¹. For the usesdescribed herein where a compound is to serve as a tag to identify anMOI, probe or primer, the mid spectral regions would be preferred. Forexample, the carbonyl stretch (1850 to 1750 cm⁻¹) would be measured forcarboxylic acids, carboxylic esters and amides, and alkyl and arylcarbonates, carbamates and ketones. N—H bending (1750 to 160 cm⁻¹) wouldbe used to identify amines, ammonium ions, and amides. At 1400 to 1250cm⁻¹, R—OH bending is detected as well as the C—N stretch in amides.Aromatic substitution patterns are detected at 900 to 690 cm⁻¹ (C—Hbending, N—H bending for ArNH₂). Saturated C—H, olefins, aromatic rings,double and triple bonds, esters, acetals, ketals, ammonium salts, N—Ocompounds such as oximes, nitro, N-oxides, and nitrates, azo,hydrazones, quinones, carboxylic acids, amides, and lactams all possessvibrational infrared correlation data (see Pretsch et al., Spectral Datafor Structure Determination of Organic Compounds, Springer-Verlag, NewYork, 1989). Preferred compounds would include an aromatic nitrile whichexhibits a very strong nitrile stretching vibration at 2230 to 2210cm⁻¹. Other useful types of compounds are aromatic alkynes which have astrong stretching vibration that gives rise to a sharp absorption bandbetween 2140 and 2100 cm⁻¹. A third compound type is the aromatic azideswhich exhibit an intense absorption band in the 2160 to 2120 cm⁻¹region. Thiocyanates are representative of compounds that have a strongabsorption at 2275 to 2263 cm⁻¹.

c. Characteristics of UV Tags

A compilation of organic chromophore types and their respectiveUV-visible properties is given in Scott (Interpretation of the UVSpectra of Natural Products, Permagon Press, New York, 1962). Achromophore is an atom or group of atoms or electrons that areresponsible for the particular light absorption. Empirical rules existfor the π to π* maxima in conjugated systems (see Pretsch et al.,Spectral Data for Structure Determination of Organic Compounds, p. B65and B70, Springer-Verlag, New York, 1989). Preferred compounds (withconjugated systems) would possess n to π* and π to π* transitions. Suchcompounds are exemplified by Acid Violet 7, Acridine Orange, AcridineYellow G, Brilliant Blue G, Congo Red, Crystal Violet, Malachite Greenoxalate, Metanil Yellow, Methylene Blue, Methyl Orange, Methyl Violet B,Naphtol Green B, Oil Blue N, Oil Red O, 4-phenylazophenol, Safranie O,Solvent Green 3, and Sudan Orange G, all of which are commerciallyavailable (Aldrich, Milwaukee, Wis.). Other suitable compounds arelisted in, e.g., Jane, I., et al., J. Chrom. 323:191-225 (1985).

d. Characteristic of a Fluorescent Tag

Fluorescent probes are identified and quantitated most directly by theirabsorption and fluorescence emission wavelengths and intensities.Emission spectra (fluorescence and phosphorescence) are much moresensitive and permit more specific measurements than absorption spectra.Other photophysical characteristics such as excited-state lifetime andfluorescence anisotropy are less widely used. The most generally usefulintensity parameters are the molar extinction coefficient (ε) forabsorption and the quantum yield (QY) for fluorescence. The value of εis specified at a single wavelength (usually the absorption maximum ofthe probe), whereas QY is a measure of the total photon emission overthe entire fluorescence spectral profile. A narrow optical bandwidth(<20 nm) is usually used for fluorescence excitation (via absorption),whereas the fluorescence detection bandwidth is much more variable,ranging from full spectrum for maximal sensitivity to narrow band (˜20nm) for maximal resolution. Fluorescence intensity per probe molecule isproportional to the product of ε and QY. The range of these parametersamong fluorophores of current practical importance is approximately10,000 to 100,000 cm⁻¹M⁻¹ for ε and 0.1 to 1.0 for QY. Compounds thatcan serve as fluorescent tags are as follows: fluorescein, rhodamine,lambda blue 470, lambda green, lambda red 664, lambda red 665, acridineorange, and propidium iodide, which are commercially available fromLambda Fluorescence Co. (Pleasant Gap, Pa.). Fluorescent compounds suchas nile red, Texas Red, lissamine™, BODIPY™s are available fromMolecular Probes (Eugene, Oreg.).

e. Characteristics of Potentiometric Tags

The principle of electrochemical detection (ECD) is based on oxidationor reduction of compounds which at certain applied voltages, electronsare either donated or accepted thus producing a current which can bemeasured. When certain compounds are subjected to a potentialdifference, the molecules undergo a molecular rearrangement at theworking electrodes' surface with the loss (oxidation) or gain(reduction) of electrons, such compounds are said to be electronic andundergo electrochemical reactions. EC detectors apply a voltage at anelectrode surface over which the HPLC eluent flows. Electroactivecompounds eluting from the column either donate electrons (oxidize) oracquire electrons (reduce) generating a current peak in real time.Importantly the amount of current generated depends on both theconcentration of the analyte and the voltage applied, with each compoundhaving a specific voltage at which it begins to oxidize or reduce. Thecurrently most popular electrochemical detector is the amperometricdetector in which the potential is kept constant and the currentproduced from the electrochemical reaction is then measured. This typeof spectrometry is currently called “potentiostatic amperometry”.Commercial amperometers are available from ESA, Inc., Chelmford, Mass.

When the efficiency of detection is 100%, the specialized detectors aretermed “coulometric”. Coulometric detectors are sensitive which have anumber of practical advantages with regard to selectivity andsensitivity which make these types of detectors useful in an array. Incoulometric detectors, for a given concentration of analyte, the signalcurrent is plotted as a function of the applied potential (voltage) tothe working electrode. The resultant sigmoidal graph is called thecurrent-voltage curve or hydrodynamic voltammagram (HDV). The HDV allowsthe best choice of applied potential to the working electrode thatpermits one to maximize the observed signal. A major advantage of ECD isits inherent sensitivity with current levels of detection in thesubfemtomole range.

Numerous chemicals and compounds are electrochemically active includingmany biochemicals, pharmaceuticals and pesticides. Chromatographicallycoeluting compounds can be effectively resolved even if their half-wavepotentials (the potential at half signal maximum) differ by only 30-60mV.

Recently developed coulometric sensors provide selectivity,identification and resolution of co-eluting compounds when used asdetectors in liquid chromatography based separations. Therefore, thesearrayed detectors add another set of separations accomplished in thedetector itself. Current instruments possess 16 channels which are inprinciple limited only by the rate at which data can be acquired. Thenumber of compounds which can be resolved on the EC array ischromatographically limited (i.e., plate count limited). However, if twoor more compounds that chromatographically co-elute have a difference inhalf wave potentials of 30-60 mV, the array is able to distinguish thecompounds. The ability of a compound to be electrochemically activerelies on the possession of an EC active group (i.e., —OH, —O, —N, —S).

Compounds which have been successfully detected using coulometricdetectors include 5-hydroxytryptamine, 3-methoxy-4-hydroxyphenyl-glycol,homogentisic acid, dopamine, metanephrine, 3-hydroxykynureninr,acetominophen, 3-hydroxytryptophol, 5-hydroxyindoleacetic acid,octanesulfonic acid, phenol, o-cresol, pyrogallol, 2-nitrophenol,4-nitrophenol, 2,4-dinitrophenol, 4,6-dinitrocresol,3-methyl-2-nitrophenol, 2,4-dichlorophenol, 2,6-dichlorophenol,2,4,5-trichlorophenol, 4-chloro-3-methylphenol, 5-methylphenol,4-methyl-2-nitrophenol, 2-hydroxyaniline, 4-hydroxyaniline,1,2-phenylenediamine, benzocatechin, buturon, chlortholuron, diuron,isoproturon, linuron, methobromuron, metoxuron, monolinuron, monuron,methionine, tryptophan, tyrosine, 4-aminobenzoic acid, 4-hydroxybenzoicacid, 4-hydroxycoumaric acid, 7-methoxycoumarin, apigenin baicalein,caffeic acid, catechin, centaurein, chlorogenic acid, daidzein,datiscetin, diosmetin, epicatechin gallate, epigallo catechin, epigallocatechin gallate, eugenol, eupatorin, ferulic acid, fisetin, galangin,gallic acid, gardenin, genistein, gentisic acid, hesperidin, irigenin,kaemferol, leucoyanidin, luteolin, mangostin, morin, myricetin,naringin, narirutin, pelargondin, peonidin, phloretin, pratensein,protocatechuic acid, rhamnetin, quercetin, sakuranetin, scutellarein,scopoletin, syringaldehyde, syringic acid, tangeritin, troxerutin,umbelliferone, vanillic acid, 1,3-dimethyl tetrahydroisoquinoline,6-hydroxydopamine, r-salsolinol, N-methyl-r-salsolinol,tetrahydroisoquinoline, amitriptyline, apomorphine, capsaicin,chlordiazepoxide, chlorpromazine, daunorubicin, desipramine, doxepin,fluoxetine, flurazepam, imipramine, isoproterenol, methoxamine,morphine, morphine-3-glucuronide, nortriptyline, oxazepam,phenylephrine, trimipramine, ascorbic acid, N-acetyl serotonin,3,4-dihydroxybenzylamine, 3,4-dihydroxymandelic acid (DOMA),3,4-dihydroxyphenylacetic acid (DOPAC), 3,4-dihydroxyphenylalanine(L-DOPA), 3,4-dihydroxyphenylglycol (DHPG), 3-hydroxyanthranilic acid,2-hydroxyphenylacetic acid (2HPAC), 4-hydroxybenzoic acid (4HBAC),5-hydroxyindole-3-acetic acid (5HIAA), 3-hydroxykynurenine,3-hydroxymandelic acid, 3-hydroxy-4-methoxyphenylethylamine,4-hydroxyphenylacetic acid (4HPAC), 4-hydroxyphenyllactic acid (4HPLA),5-hydroxytryptophan (5HTP), 5-hydroxytryptophol (5HTOL),5-hydroxytryptamine (5HT), 5-hydroxytryptamine sulfate,3-methoxy-4-hydroxyphenylglycol (MHPG), 5-methoxytryptamine,5-methoxytryptophan, 5-methoxytryptophol, 3-methoxytyramine (3MT),3-methoxytyrosine (3-OM-DOPA), 5-methylcysteine, 3-methylguanine,bufotenin, dopamine dopamine-3-glucuronide, dopamine-3-sulfate,dopamine-4-sulfate, epinephrine, epinine, folic acid, glutathione(reduced), guanine, guanosine, homogentisic acid (HGA), homovanillicacid (HVA), homovanillyl alcohol (HVOL), homoveratic acid, hva sulfate,hypoxanthine, indole, indole-3-acetic acid, indole-3-lactic acid,kynurenine, melatonin, metanephrine, N-methyltryptamine,N-methyltyramine, N,N-dimethyltryptamine, N,N-dimethyltyramine,norepinephrine, normetanephrine, octopamine, pyridoxal, pyridoxalphosphate, pyridoxamine, synephrine, tryptophol, tryptamine, tyramine,uric acid, vanillylmandelic acid (vma), xanthine and xanthosine. Othersuitable compounds are set forth in, e.g., Jane, I., et al. J. Chrom.323:191-225 (1985) and Musch, G., et al., J. Chrom. 348:97-110 (1985).These compounds can be incorporated into compounds of formula T—L—X bymethods known in the art. For example, compounds having a carboxylicacid group may be reacted with amine, hydroxyl, etc. to form amide,ester and other linkages between T and L.

In addition to the above properties, and regardless of the intendeddetection method, it is preferred that the tag have a modular chemicalstructure. This aids in the construction of large numbers ofstructurally related tags using the techniques of combinatorialchemistry. For example, the T^(ms) group desirably has severalproperties. It desirably contains a functional group which supports asingle ionized charge state when the T^(ms)-containing moiety issubjected to mass spectrometry (more simply referred to as a “mass specsensitivity enhancer” group, or MSSE). Also, it desirably can serve asone member in a family of T^(ms)-containing moieties, where members ofthe family each have a different mass/charge ratio, however haveapproximately the same sensitivity in the mass spectrometer. Thus, themembers of the family desirably have the same MSSE. In order to allowthe creation of families of compounds, it has been found convenient togenerate tag reactants via a modular synthesis scheme, so that the tagcomponents themselves may be viewed as comprising modules.

In a preferred modular approach to the structure of the T^(ms) group,T^(ms) has the formula

T²—(J—T³—)_(n)—

wherein T² is an organic moiety formed from carbon and one or more ofhydrogen, fluoride, iodide, oxygen, nitrogen, sulfur and phosphorus,having a mass range of 15 to 500 daltons; T³ is an organic moiety formedfrom carbon and one or more of hydrogen, fluoride, iodide, oxygen,nitrogen, sulfur and phosphorus, having a mass range of 50 to 1000daltons; J is a direct bond or a functional group such as amide, ester,amine, sulfide, ether, thioester, disulfide, thioether, urea, thiourea,carbamate, thiocarbamate, Schiff base, reduced Schiff base, imine,oxime, hydrazone, phosphate, phosphonate, phosphoramide, phosphonamide,sulfonate, sulfonamide or carbon-carbon bond; and n is an integerranging from 1 to 50, such that when n is greater than 1, each T³ and Jis independently selected.

The modular structure T²—(J—T³)_(n)— provides a convenient entry tofamilies of T—L—X compounds, where each member of the family has adifferent T group. For instance, when T is T^(ms), and each familymember desirably has the same MSSE, one of the T³ groups can providethat MSSE structure. In order to provide variability between members ofa family in terms of the mass of T^(ms), the T² group may be variedamong family members. For instance, one family member may haveT²=methyl, while another has T²=ethyl, and another has T²=propyl, etc.

In order to provide “gross” or large jumps in mass, a T³ group may bedesigned which adds significant (e.g., one or several hundreds) of massunits to T—L—X. Such a T³ group may be referred to as a molecular weightrange adjuster group(“WRA”). A WRA is quite useful if one is workingwith a single set of T² groups, which will have masses extending over alimited range. A single set of T² groups may be used to create T^(ms)groups having a wide range of mass simply by incorporating one or moreWRA T³ groups into the T^(ms). Thus, using a simple example, if a set ofT² groups affords a mass range of 250-340 daltons for the T^(ms), theaddition of a single WRA, having, as an exemplary number 100 dalton, asa T³ group provides access to the mass range of 350-440 daltons whileusing the same set of T² groups. Similarly, the addition of two 100dalton MWA groups (each as a T³ group) provides access to the mass rangeof 450-540 daltons, where this incremental addition of WRA groups can becontinued to provide access to a very large mass range for the T^(ms)group. Preferred compounds of the formula T²—(J—T³—)_(n)—L—X have theformula R_(VWC)—(R_(WRA))_(w)—R_(MSSE)—L—X where VWC is a “T²” group,and each of the WRA and MSSE groups are “T³” groups. This structure isillustrated in FIG. 12, and represents one modular approach to thepreparation of T^(ms).

In the formula T²—(J—T³—)_(n)—, T² and T³ are preferably selected fromhydrocarbyl, hydrocarbyl-O-hydrocarbylene, hydrocarbyl-S-hydrocarbylene,hydrocarbyl-NH-hydrocarbylene, hydrocarbyl-amide-hydrocarbylene,N-(hydrocarbyl)hydrocarbylene, N,N-di(hydrocarbyl)hydrocarbylene,hydrocarbylacylhydrocarbylene, heterocyclylhydrocarbyl wherein theheteroatom(s) are selected from oxygen, nitrogen, sulfur and phosphorus,substituted heterocyclylhydrocarbyl wherein the heteroatom(s) areselected from oxygen, nitrogen, sulfur and phosphorus and thesubstituents are selected from hydrocarbyl,hydrocarbyl-O-hydrocarbylene, hydrocarbyl-NH-hydrocarbylene,hydrocarbyl-S-hydrocarbylene, N-(hydrocarbyl)hydrocarbylene,N,N-di(hydrocarbyl)hydrocarbylene and hydrocarbylacyl-hydrocarbylene. Inaddition, T² and/or T³ may be a derivative of any of the previouslylisted potential T²/T³ groups, such that one or more hydrogens arereplaced fluorides.

Also regarding the formula T²—(J—T³—)_(n)—, a preferred T³ has theformula —G(R²)—, wherein G is C₁₋₆ alkylene chain having a single R²substituent. Thus, if G is ethylene (—CH₂—CH₂—) either one of the twoethylene carbons may have a R² substituent, and R² is selected fromalkyl, alkenyl, alkynyl, cycloalkyl, aryl-fused cycloalkyl,cycloalkenyl, aryl, aralkyl, aryl-substituted alkenyl or alkynyl,cycloalkyl-substituted alkyl, cycloalkenyl-substituted cycloalkyl,biaryl, alkoxy, alkenoxy, alkynoxy, aralkoxy, aryl-substituted alkenoxyor alkynoxy, alkylamino, alkenylamino or alkynylamino, aryl-substitutedalkylamino, aryl-substituted alkenylamino or alkynylamino, aryloxy,arylamino, N-alkylurea-substituted alkyl, N-arylurea-substituted alkyl,alkylcarbonylamino-substituted alkyl, aminocarbonyl-substituted alkyl,heterocyclyl, heterocyclyl-substituted alkyl, heterocyclyl-substitutedamino, carboxyalkyl substituted aralkyl, oxocarbocyclyl-fused aryl andheterocyclylalkyl; cycloalkenyl, aryl-substituted alkyl and, aralkyl,hydroxy-substituted alkyl, alkoxy-substituted alkyl,aralkoxy-substituted alkyl, alkoxy-substituted alkyl,aralkoxy-substituted alkyl, amino-substituted alkyl, (aryl-substitutedalkyloxycarbonylamino)-substituted alkyl, thiol-substituted alkyl,alkylsulfonyl-substituted alkyl, (hydroxy-substitutedalkylthio)-substituted alkyl, thioalkoxy-substituted alkyl,hydrocarbylacylamino-substituted alkyl,heterocyclylacylamino-substituted alkyl,hydrocarbyl-substituted-heterocyclylacylamino-substituted alkyl,alkylsulfonylamino-substituted alkyl, arylsulfonylamino-substitutedalkyl, morpholino-alkyl, thiomorpholino-alkyl, morpholinocarbonyl-substituted alkyl, thiomorpholinocarbonyl-substituted alkyl,[N-(alkyl, alkenyl or alkynyl)- or N,N-[dialkyl, dialkenyl, dialkynyl or(alkyl, alkenyl)-amino]carbonyl-substituted alkyl,heterocyclylaminocarbonyl, heterocylylalkyleneaminocarbonyl,heterocyclylaminocarbonyl-substituted alkyl,heterocylylalkyleneaminocarbonyl-substituted alkyl,N,N-[dialkyl]alkyleneaminocarbonyl,N,N-[dialkyl]alkyleneaminocarbonyl-substituted alkyl, alkyl-substitutedheterocyclylcarbonyl, alkyl-substituted heterocyclylcarbonyl-alkyl,carboxyl-substituted alkyl, dialkylamino-substituted acylaminoalkyl andamino acid side chains selected from arginine, asparagine, glutamine,S-methyl cysteine, methionine and corresponding sulfoxide and sulfonederivatives thereof, glycine, leucine, isoleucine, allo-isoleucine,tert-leucine, norleucine, phenylalanine, tyrosine, tryptophan, proline,alanine, omithine, histidine, glutamine, valine, threonine, serine,aspartic acid, beta-cyanoalanine, and allothreonine; alynyl andheterocyclylcarbonyl, aminocarbonyl, amido, mono- ordialkylaminocarbonyl, mono- or diarylaminocarbonyl,alkylarylaminocarbonyl, diarylaminocarbonyl, mono- ordiacylaminocarbonyl, aromatic or aliphatic acyl, alkyl optionallysubstituted by substituents selected from amino, carboxy, hydroxy,mercapto, mono- or dialkylamino, mono- or diarylamino, alkylarylamino,diarylamino, mono- or diacylamino, alkoxy, alkenoxy, aryloxy,thioalkoxy, thioalkenoxy, thioalkynoxy, thioaryloxy and heterocyclyl.

A preferred compound of the formula T²—(J—T³—)_(n)—L—X has thestructure:

wherein G is (CH₂)₁₋₆ such that a hydrogen on one and only one of theCH₂ groups represented by a single “G” is replacedwith-(CH₂)_(c)-Amide-T⁴; T² and T⁴ are organic moieties of the formulaC₁₋₂₅N₀₋₉O₀₋₉H_(α)F_(β) such that the sum of α and β is sufficient tosatisfy the otherwise unsatisfied valencies of the C, N, and O atoms;amide is

R¹ is hydrogen or C₁₋₁₀ alkyl; c is an integer ranging from 0 to 4; andn is an integer ranging from 1 to 50 such that when n is greater than 1,G, c, Amide, R¹ and T⁴ are independently selected.

In a further preferred embodiment, a compound of the formulaT²—(J—T³—)_(n)—L—X has the structure:

wherein T⁵ is an organic moiety of the formula C₁₋₂₅N₀₋₉O₀₋₉H_(α)F_(β)such that the sum of α and β is sufficient to satisfy the otherwiseunsatisfied valencies of the C, N, and O atoms; and T⁵ includes atertiary or quaternary amine or an organic acid; m is an integer rangingfrom 0-49, and T², T⁴, R¹, L and X have been previously defined.

Another preferred compound having the formula T²—(J—T³—)_(n)—L—X has theparticular structure:

wherein T⁵ is an organic moiety of the formula C₁₋₂₅N₀₋₉O₀₋₉H_(α)F_(β)such that the sum of α and β is sufficient to satisfy the otherwiseunsatisfied valencies of the C, N, and O atoms; and T⁵ includes atertiary or quaternary amine or an organic acid; m is an integer rangingfrom 0-49, and T², T⁴, c, R¹, “Amide”, L and X have been previouslydefined.

In the above structures that have a T⁵ group, -Amide-T⁵ is preferablyone of the following, which are conveniently made by reacting organicacids with free amino groups extending from “G”:

Where the above compounds have a T⁵ group, and the “G” group has a freecarboxyl group (or reactive equivalent thereof), then the following arepreferred -Amide-T⁵ group, which may conveniently be prepared byreacting the appropriate organic amine with a free carboxyl groupextending from a “G” group:

In three preferred embodiments of the invention, T—L—MOI has thestructure:

or the structure:

or the structure:

wherein T² and T⁴ are organic moieties of the formulaC₁₋₂₅N₀₋₉O₀₋₉S₀₋₃P₀₋₃H_(α)F_(β)I_(δ) such that the sum of α, β and δ issufficient to satisfy the otherwise unsatisfied valencies of the C, N,O, S and P atoms; G is (CH₂)₁₋₆ wherein one and only one hydrogen on theCH₂ groups represented by each G is replaced with —(CH₂)_(c)-Amide-T⁴;Amide is

R¹ is hydrogen or C₁₋₁₀ alkyl; c is an integer ranging from 0 to 4;“C₂-C₁₀” represents a hydrocarbylene group having from 2 to 10 carbonatoms, “ODN-3′—OH” represents a nucleic acid fragment having a terminal3′ hydroxyl group (i.e., a nucleic acid fragment joined to (C₁-C₁₀) atother than the 3′ end of the nucleic acid fragment); and n is an integerranging from 1 to 50 such that when n is greater than 1, then G, c,Amide, R¹ and T⁴ are independently selected. Preferably there are notthree heteroatoms bonded to a single carbon atom.

In structures as set forth above that contain a T²—C(═O)—N(R¹)— group,this group may be formed by reacting an amine of the formula HN(R¹)—with an organic acid selected from the following, which are exemplaryonly and do not constitute an exhaustive list of potential organicacids: Formic acid, Acetic acid, Propiolic acid, Propionic acid,Fluoroacetic acid, 2-Butynoic acid, Cyclopropanecarboxylic acid, Butyricacid, Methoxyacetic acid, Difluoroacetic acid, 4-Pentynoic acid,Cyclobutanecarboxylic acid, 3,3-Dimethylacrylic acid, Valeric acid,N,N-Dimethylglycine, N-Formyl-Gly-OH, Ethoxyacetic acid,(Methylthio)acetic acid, Pyrrole-2-carboxylic acid, 3-Furoic acid,Isoxazole-5-carboxylic acid, trans-3-Hexenoic acid, Trifluoroaceticacid, Hexanoic acid, Ac-Gly-OH, 2-Hydroxy-2-methylbutyric acid, Benzoicacid, Nicotinic acid, 2-Pyrazinecarboxylic acid,1-Methyl-2-pyrrolecarboxylic acid, 2-Cyclopentene-1-acetic acid,Cyclopentylacetic acid, (S)-(−)-2-Pyrrolidone-5-carboxylic acid,N-Methyl-L-proline, Heptanoic acid, Ac-b-Ala-OH,2-Ethyl-2-hydroxybutyric acid, 2-(2-Methoxyethoxy)acetic acid, p-Toluicacid, 6-Methylnicotinic acid, 5-Methyl-2-pyrazinecarboxylic acid,2,5-Dimethylpyrrole-3-carboxylic acid, 4-Fluorobenzoic acid,3,5-Dimethylisoxazole-4-carboxylic acid, 3-Cyclopentylpropionic acid,Octanoic acid, N,N-Dimethylsuccinamic acid, Phenylpropiolic acid,Cinnamic acid, 4-Ethylbenzoic acid, p-Anisic acid,1,2,5-Trimethylpyrrole-3-carboxylic acid, 3-Fluoro-4-methylbenzoic acid,Ac-DL-Propargylglycine, 3-(Trifluoromethyl)butyric acid,1-Piperidinepropionic acid, N-Acetylproline, 3,5-Difluorobenzoic acid,Ac-L-Val-OH, Indole-2-carboxylic acid, 2-Benzofurancarboxylic acid,Benzotriazole-5-carboxylic acid, 4-n-Propylbenzoic acid,3-Dimethylaminobenzoic acid, 4-Ethoxybenzoic acid, 4-(Methylthio)benzoicacid, N-(2-Furoyl)glycine, 2-(Methylthio)nicotinic acid,3-Fluoro-4-methoxybenzoic acid, Tfa-Gly-OH, 2-Napthoic acid, Quinaldicacid, Ac-L-Ile-OH, 3-Methylindene-2-carboxylic acid,2-Quinoxalinecarboxylic acid, 1-Methylindole-2-carboxylic acid,2,3,6-Trifluorobenzoic acid, N-Formyl-L-Met-OH,2-[2-(2-Methoxyethoxy)ethoxy]acetic acid, 4-n-Butylbenzoic acid,N-Benzoylglycine, 5-Fluoroindole-2-carboxylic acid, 4-n-Propoxybenzoicacid, 4-Acetyl-3,5-dimethyl-2-pyrrolecarboxylic acid,3,5-Dimethoxybenzoic acid, 2,6-Dimethoxynicotinic acid,Cyclohexanepentanoic acid, 2-Naphthylacetic acid,4-(1H-Pyrrol-1-yl)benzoic acid, Indole-3-propionic acid,m-Trifluoromethylbenzoic acid, 5-Methoxyindole-2-carboxylic acid,4-Pentylbenzoic acid, Bz-b-Ala-OH, 4-Diethylaminobenzoic acid,4-n-Butoxybenzoic acid, 3-Methyl-5-CF3-isoxazole-4-carboxylic acid,(3,4-Dimethoxyphenyl)acetic acid, 4-Biphenylcarboxylic acid,Pivaloyl-Pro-OH, Octanoyl-Gly-OH, (2-Naphthoxy)acetic acid,Indole-3-butyric acid, 4-(Trifluoromethyl)phenylacetic acid,5-Methoxyindole-3-acetic acid, 4-(Trifluoromethoxy)benzoic acid,Ac-L-Phe-OH, 4-Pentyloxybenzoic acid, Z-Gly-OH,4-Carboxy-N-(fur-2-ylmethyl)pyrrolidin-2-one, 3,4-Diethoxybenzoic acid,2,4-Dimethyl-5-CO₂Et-pyrrole-3-carboxylic acid,N-(2-Fluorophenyl)succinamic acid, 3,4,5-Trimethoxybenzoic acid,N-Phenylanthranilic acid, 3-Phenoxybenzoic acid, Nonanoyl-Gly-OH,2-Phenoxypyridine-3-carboxylic acid,2,5-Dimethyl-1-phenylpyrrole-3-carboxylic acid,trans-4-(Trifluoromethyl)cinnamic acid,(5-Methyl-2-phenyloxazol-4-yl)acetic acid, 4-(2-Cyclohexenyloxy)benzoicacid, 5-Methoxy-2-methylindole-3-acetic acid, trans-4-Cotininecarboxylicacid, Bz-5-Aminovaleric acid, 4-Hexyloxybenzoic acid,N-(3-Methoxyphenyl)succinamic acid, Z-Sar-OH,4-(3,4-Dimethoxyphenyl)butyric acid, Ac-o-Fluoro-DL-Phe-OH,N-(4-Fluorophenyl)glutaramic acid, 4′-Ethyl-4-biphenylcarboxylic acid,1,2,3,4-Tetrahydroacridinecarboxylic acid, 3-Phenoxyphenylacetic acid,N-(2,4-Difluorophenyl)succinamic acid, N-Decanoyl-Gly-OH,(+)-6-Methoxy-a-methyl-2-naphthaleneacetic acid,3-(Trifluoromethoxy)cinnamic acid, N-Formyl-DL-Trp-OH,(R)-(+)-a-Methoxy-a-(trifluoromethyl)phenylacetic acid, Bz-DL-Leu-OH,4-(Trifluoromethoxy)phenoxyacetic acid, 4-Heptyloxybenzoic acid,2,3,4-Trimethoxycinnamic acid, 2,6-Dimethoxybenzoyl-Gly-OH,3-(3,4,5-Trimethoxyphenyl)propionic acid,2,3,4,5,6-Pentafluorophenoxyacetic acid,N-(2,4-Difluorophenyl)glutaramic acid, N-Undecanoyl-Gly-OH,2-(4-Fluorobenzoyl)benzoic acid, 5-Trifluoromethoxyindole-2-carboxylicacid, N-(2,4-Difluorophenyl)diglycolamic acid, Ac-L-Trp-OH,Tfa-L-Phenylglycine-OH, 3-Iodobenzoic acid,3-(4-n-Pentylbenzoyl)propionic acid, 2-Phenyl-4-quinolinecarboxylicacid, 4-Octyloxybenzoic acid, Bz-L-Met-OH, 3,4,5-Triethoxybenzoic acid,N-Lauroyl-Gly-OH, 3,5-Bis(trifluoromethyl)benzoic acid,Ac-5-Methyl-DL-Trp-OH, 2-Iodophenylacetic acid, 3-Iodo-4-methylbenzoicacid, 3-(4-n-Hexylbenzoyl)propionic acid, N-Hexanoyl-L-Phe-OH,4-Nonyloxybenzoic acid, 4′-(Trifluoromethyl)-2-biphenylcarboxylic acid,Bz-L-Phe-OH, N-Tridecanoyl-Gly-OH, 3,5-Bis(trifluoromethyl)phenylaceticacid, 3-(4-n-Heptylbenzoyl)propionic acid, N-Hepytanoyl-L-Phe-OH,4-Decyloxybenzoic acid, N-(α,α,α-trifluoro-m-tolyl)anthranilic acid,Niflumic acid, 4-(2-Hydroxyhexafluoroisopropyl)benzoic acid,N-Myristoyl-Gly-OH, 3-(4-n-Octylbenzoyl)propionic acid,N-Octanoyl-L-Phe-OH, 4-Undecyloxybenzoic acid,3-(3,4,5-Trimethoxyphenyl)propionyl-Gly-OH, 8-Iodonaphthoic acid,N-Pentadecanoyl-Gly-OH, 4-Dodecyloxybenzoic acid, N-Palmitoyl-Gly-OH,and N-Stearoyl-Gly-OH. These organic acids are available from one ormore of Advanced ChemTech, Louisville, Ky.; Bachem Bioscience Inc.,Torrance, Calif.; Calbiochem-Novabiochem Corp., San Diego, Calif.;Farchan Laboratories Inc., Gainesville Fla.; Lancaster Synthesis,Windham N.H.; and MayBridge Chemical Company (c/o Ryan Scientific),Columbia, S.C. The catalogs from these companies use the abreviationswhich are used above to identify the acids.

f. Combinatorial Chemistry as a Means for Preparing Tags

Combinatorial chemistry is a type of synthetic strategy which leads tothe production of large chemical libraries (see, for example, PCTApplication Publication No. WO 94/08051). These combinatorial librariescan be used as tags for the identification of molecules of interest(MOIs). Combinatorial chemistry may be defined as the systematic andrepetitive, covalent connection of a set of different “building blocks”of varying structures to each other to yield a large array of diversemolecular entities. Building blocks can take many forms, both naturallyoccurring and synthetic, such as nucleophiles, electrophiles, dienes,alkylating or acylating agents, diamines, nucleotides, amino acids,sugars, lipids, organic monomers, synthons, and combinations of theabove. Chemical reactions used to connect the building blocks mayinvolve alkylation, acylation, oxidation, reduction, hydrolysis,substitution, elimination, addition, cyclization, condensation, and thelike. This process can produce libraries of compounds which areoligomeric, non-oligomeric, or combinations thereof. If oligomeric, thecompounds can be branched, unbranched, or cyclic. Examples of oligomericstructures which can be prepared by combinatorial methods includeoligopeptides, oligonucleotides, oligosaccharides, polylipids,polyesters, polyamides, polyurethanes, polyureas, polyethers,poly(phosphorus derivatives), e.g., phosphates, phosphonates,phosphoramides, phosphonamides, phosphites, phosphinamides, etc., andpoly(sulfur derivatives), e.g., sulfones, sulfonates, sulfites,sulfonamides, sulfenamides, etc.

One common type of oligomeric combinatorial library is the peptidecombinatorial library. Recent innovations in peptide chemistry andmolecular biology have enabled libraries consisting of tens to hundredsof millions of different peptide sequences to be prepared and used. Suchlibraries can be divided into three broad categories. One category oflibraries involves the chemical synthesis of soluble non-support-boundpeptide libraries (e.g., Houghten et al., Nature 354:84, 1991). A secondcategory involves the chemical synthesis of support-bound peptidelibraries, presented on solid supports such as plastic pins, resinbeads, or cotton (Geysen et al., Mol. Immunol. 23:709, 1986; Lam et al.,Nature 354:82, 1991; Eichler and Houghten, Biochemistry 32:11035, 1993).In these first two categories, the building blocks are typically L-aminoacids, D-amino acids, unnatural amino acids, or some mixture orcombination thereof. A third category uses molecular biology approachesto prepare peptides or proteins on the surface of filamentous phageparticles or plasmids (Scott and Craig, Curr. Opinion Biotech. 5:40,1994). Soluble, nonsupport-bound peptide libraries appear to be suitablefor a number of applications, including use as tags. The availablerepertoire of chemical diversities in peptide libraries can be expandedby steps such as permethylation (Ostresh et al., Proc. Natl. Acad. Sci.,USA 91:11138, 1994).

Numerous variants of peptide combinatorial libraries are possible inwhich the peptide backbone is modified, and/or the amide bonds have beenreplaced by mimetic groups. Amide mimetic groups which may be usedinclude ureas, urethanes, and carbonylmethylene groups. Restructuringthe backbone such that sidechains emanate from the amide nitrogens ofeach amino acid, rather than the alpha-carbons, gives libraries ofcompounds known as peptoids (Simon et al., Proc. Natl. Acad Sci., USA89:9367, 1992).

Another common type of oligomeric combinatorial library is theoligonucleotide combinatorial library, where the building blocks aresome form of naturally occurring or unnatural nucleotide orpolysaccharide derivatives, including where various organic andinorganic groups may substitute for the phosphate linkage, and nitrogenor sulfur may substitute for oxygen in an ether linkage (Schneider etal., Biochem. 34:9599, 1995; Freier et al., J. Med. Chem. 38:344, 1995;Frank, J. Biotechnology 41:259, 1995; Schneider et al., Published PCT WO942052; Ecker et al., Nucleic Acids Res. 21:1853, 1993).

More recently, the combinatorial production of collections ofnon-oligomeric, small molecule compounds has been described (DeWitt etal., Proc. Natl. Acad. Sci., USA 90:690, 1993; Bunin et al., Proc. Natl.Acad. Sci., USA 91:4708, 1994). Structures suitable for elaboration intosmall-molecule libraries encompass a wide variety of organic molecules,for example heterocyclics, aromatics, alicyclics, aliphatics, steroids,antibiotics, enzyme inhibitors, ligands, hormones, drugs, alkaloids,opioids, terpenes, porphyrins, toxins, catalysts, as well ascombinations thereof.

g. Specific Methods for Combinatorial Synthesis of Tags

Two methods for the preparation and use of a diverse set ofamine-containing MS tags are outlined below. In both methods, solidphase synthesis is employed to enable simultaneous parallel synthesis ofa large number of tagged linkers, using the techniques of combinatorialchemistry. In the first method, the eventual cleavage of the tag fromthe oligonucleotide results in liberation of a carboxyl amide. In thesecond method, cleavage of the tag produces a carboxylic acid. Thechemical components and linking elements used in these methods areabbreviated as follows:

R=resin

FMOC=fluorenylmethoxycarbonyl protecting group

All=allyl protecting group

CO₂H=carboxylic acid group

CONH₂=carboxylic amide group

NH₂=amino group

OH=hydroxyl group

CONH=amide linkage

COO=ester linkage

NH₂-Rink-CO₂H=4-[(α-amino)-2,4-dimethoxybenzyl]-phenoxybutyric acid(Rink linker)

OH-1MeO—CO₂H=(4-hydroxymethyl)phenoxybutyric acid

OH-2MeO—CO₂H=(4-hydroxymethyl-3-methoxy)phenoxyacetic acid

NH₂—A—COOH=amino acid with aliphatic or aromatic amine functionality inside chain

X1 . . . Xn-COOH=set of n diverse carboxylic acids with unique molecularweights

oligo1 . . . oligo(n)=set of n oligonucleotides

HBTU=O-benzotriazol-1-yl-N,N,N′,N′-tetramethyluroniumhexafluorophosphate

The sequence of steps in Method 1 is as follows:

OH—2MeO—CONH—R ↓ FMOC—NH—Rink—CO₂H; couple (e.g., HBTU)FMOC—NH—Rink—COO—2MeO—CONH—R ↓ piperidine (remove FMOC)NH₂—Rink—COO—2MeO—CONH—R ↓ FMOC—NH—A—COOH; couple (e.g., HBTU)FMOC—NH—A—CONH—Rink—COO—2MeO—CONH—R ↓ piperidine (remove FMOC)NH₂—A—CONH—Rink—COO—2MeO—CONH—R ↓ divide into n aliquots ↓↓↓↓↓ couple ton different acids X1 . . . Xn—COOH X1 . . .Xn—CONH—A—CONH—Rink—COO—2MeO—CONH—R ↓↓↓↓↓ Cleave tagged linkers fromresin with 1% TFA X1 . . . Xn—CONH—A—CONH—Rink—CO₂H ↓↓↓↓↓ couple to noligos (oligo1 . . . oligo(n)) (e.g, via Pfp esters) X1 . . .Xn—CONH—A—CONH—Rink—CONH-oligo1 . . . oligo(n) ↓ pool tagged oligos ↓perform sequencing reaction ↓ separate different length fragments fromsequencing reaction (e.g, via HPLC or CE) ↓ cleave tags from linkerswith 25%-100% TFA X1 . . . Xn—CONH—A—CONH ↓ analyze by mass spectrometry

The sequence of steps in Method 2 is as follows:

OH—1MeO—CO₂-All ↓ FMOC—NH—A—CO₂H; couple (e.g., HBTU)FMOC—NH—A—COO—1MeO—CO₂—All ↓ Palladium (remove Allyl)FMOC—NH—A—COO—1MeO—CO₂H ↓ OH—2MeO—CONH—R; couple (e.g, HBTU)FMOC—NH—A—COO—1MeO—COO—2MeO—CONH—R ↓ piperidine (remove FMOC)NH₂—A—COO—1MeO—COO—2MeO—CONH—R ↓ divide into n aliquots ↓↓↓↓↓ couple ton different acids X1 . . . Xn—CO₂H X1 . . .Xn—CONH—A—COO—1MeO—COO—2MeO—CONH—R ↓↓↓↓↓ cleave tagged linkers fromresin with 1% TFA X1 . . . Xn—CONH—A—COO—1MeO—CO₂H ↓↓↓↓↓ couple to noligos (oligo1 . . . oligo(n)) (e.g., via Pfp esters) X1 . . .Xn—CONH—A—COO—1MeO—CONH-oligo1 . . . oligo(n) ↓ pool tagged oligos ↓perform sequencing reaction ↓ separate different length fragments fromsequencing reaction (e.g, via HPLC orCE) ↓ cleave tags from linkers with25-100% TFA X1 . . . Xn—CONH—A—CO₂H ↓ analyze by mass spectrometry

2. Linkers

A “linker” component (or L), as used herein, means either a directcovalent bond or an organic chemical group which is used to connect a“tag” (or T) to a “molecule of interest” (or MOI) through covalentchemical bonds. In addition, the direct bond itself, or one or morebonds within the linker component is cleavable under conditions whichallows T to be released (in other words, cleaved) from the remainder ofthe T—L—X compound (including the MOI component). The tag variablecomponent which is present within T should be stable to the cleavageconditions. Preferably, the cleavage can be accomplished rapidly; withina few minutes and preferably within about 15 seconds or less.

In general, a linker is used to connect each of a large set of tags toeach of a similarly large set of MOIs. Typically, a single tag-linkercombination is attached to each MOI (to give various T—L—MOI), but insome cases, more than one tag-linker combination may be attached to eachindividual MOI (to give various (T—L)n-MOI). In another embodiment ofthe present invention, two or more tags are bonded to a single linkerthrough multiple, independent sites on the linker, and this multipletag-linker combination is then bonded to an individual MOI (to givevarious (T)n-L—MOI).

After various manipulations of the set of tagged MOIs, special chemicaland/or physical conditions are used to cleave one or more covalent bondsin the linker, resulting in the liberation of the tags from the MOIs.The cleavable bond(s) may or may not be some of the same bonds that wereformed when the tag, linker, and MOI were connected together. The designof the linker will, in large part, determine the conditions under whichcleavage may be accomplished. Accordingly, linkers may be identified bythe cleavage conditions they are particularly susceptible too. When alinker is photolabile (i.e., prone to cleavage by exposure to actinicradiation), the linker may be given the designation L^(hν). Likewise,the designations L^(acid), L^(base), L^([O]), L^([R]), L^(enz), L^(elc),L^(Δ) and L^(ss) may be used to refer to linkers that are particularlysusceptible to cleavage by acid, base, chemical oxidation, chemicalreduction, the catalytic activity of an enzyme (more simply “enzyme”),electrochemical oxidation or reduction, elevated temperature (“thermal”)and thiol exchange, respectively.

Certain types of linker are labile to a single type of cleavagecondition, whereas others are labile to several types of cleavageconditions. In addition, in linkers which are capable of bondingmultiple tags (to give (T)n-L—MOI type structures), each of thetag-bonding sites may be labile to different cleavage conditions. Forexample, in a linker having two tags bonded to it, one of the tags maybe labile only to base, and the other labile only to photolysis.

A linker which is useful in the present invention possesses severalattributes:

1) The linker possesses a chemical handle (L_(h)) through which it canbe attached to an MOI.

2) The linker possesses a second, separate chemical handle (L_(h))through which the tag is attached to the linker. If multiple tags areattached to a single linker ((T)n-L—MOI type structures), then aseparate handle exists for each tag.

3) The linker is stable toward all manipulations to which it issubjected, with the exception of the conditions which allow cleavagesuch that a T-containing moiety is released from the remainder of thecompound, including the MOI. Thus, the linker is stable duringattachment of the tag to the linker, attachment of the linker to theMOI, and any manipulations of the MOI while the tag and linker (T—L) areattached to it.

4) The linker does not significantly interfere with the manipulationsperformed on the MOI while the T—L is attached to it. For instance, ifthe T—L is attached to an oligonucleotide, the T—L must notsignificantly interfere with any hybridization or enzymatic reactions(e.g., PCR) performed on the oligonucleotide. Similarly, if the T—L isattached to an antibody, it must not significantly interfere withantigen recognition by the antibody.

5) Cleavage of the tag from the remainder of the compound occurs in ahighly controlled manner, using physical or chemical processes that donot adversely affect the detectability of the tag.

For any given linker, it is preferred that the linker be attachable to awide variety of MOIs, and that a wide variety of tags be attachable tothe linker. Such flexibility is advantageous because it allows a libraryof T—L conjugates, once prepared, to be used with several different setsof MOIs.

As explained above, a preferred linker has the formula

L_(h)—L¹—L²—L³—L_(h)

wherein each L_(h) is a reactive handle that can be used to link thelinker to a tag reactant and a molecule of interest reactant. L² is anessential part of the linker, because L² imparts lability to the linker.L¹ and L³ are optional groups which effectively serve to separate L²from the handles L_(h).

L¹ (which, by definition, is nearer to T than is L³), serves to separateT from the required labile moiety L². This separation may be useful whenthe cleavage reaction generates particularly reactive species (e.g.,free radicals) which may cause random changes in the structure of theT-containing moiety. As the cleavage site is further separated from theT-containing moiety, there is a reduced likelihood that reactive speciesformed at the cleavage site will disrupt the structure of theT-containing moiety. Also, as the atoms in L1 will typically be presentin the T-containing moiety, these L¹ atoms may impart a desirablequality to the T-containing moiety. For example, where the T-containingmoiety is a T^(ms)-containing moiety, and a hindered amine is desirablypresent as part of the structure of the T^(ms)-containing moiety (toserve, e.g., as a MSSE), the hindered amine may be present in L¹ labilemoiety.

In other instances, L¹ and/or L³ may be present in a linker componentmerely because the commercial supplier of a linker chooses to sell thelinker in a form having such a L¹ and/or L³ group. In such an instance,there is no harm in using linkers having L¹ and/or L³ groups, (so longas these group do not inhibit the cleavage reaction) even though theymay not contribute any particular performance advantage to the compoundsthat incorporate them. Thus, the present invention allows for L¹ and/orL³ groups to be present in the linker component.

L¹ and/or L³ groups may be a direct bond (in which case the group iseffectively not present), a hydrocarbylene group (e.g., alkylene,arylene, cycloalkylene, etc.), —O-hydrocarbylene (e.g., —O—CH₂—,O—CH₂CH(CH₃)—, etc.) or hydrocarbylene-(O-hydrocarbylene)_(w)- wherein wis an integer ranging from 1 to about 10 (e.g., —CH₂—O—Ar—,—CH₂—(O—CH₂CH₂)₄—, etc.).

With the advent of solid phase synthesis, a great body of literature hasdeveloped regarding linkers that are labile to specific reactionconditions. In typical solid phase synthesis, a solid support is bondedthrough a labile linker to a reactive site, and a molecule to besynthesized is generated at the reactive site. When the molecule hasbeen completely synthesized, the solid support-linker-molecule constructis subjected to cleavage conditions which releases the molecule from thesolid support. The labile linkers which have been developed for use inthis context (or which may be used in this context) may also be readilyused as the linker reactant in the present invention.

Lloyd-Williams, P., et al., “Convergent Solid-Phase Peptide Synthesis”,Tetrahedron Report No. 347, 49(48):11065-11133 (1993) provides anextensive discussion of linkers which are labile to actinic radiation(i.e., photolysis), as well as acid, base and other cleavage conditions.Additional sources of information about labile linkers may be readilyobtained.

As described above, different linker designs will confer cleavability(“lability”) under different specific physical or chemical conditions.Examples of conditions which serve to cleave various designs of linkerinclude acid, base, oxidation, reduction, fluoride, thiol exchange,photolysis, and enzymatic conditions.

Examples of cleavable linkers that satisfy the general criteria forlinkers listed above will be well known to those in the art and includethose found in the catalog available from Pierce (Rockford, Ill).Examples include:

ethylene glycobis(succinimidylsuccinate) (EGS), an amine reactivecross-linking reagent which is cleavable by hydroxylamine (1 M at 37° C.for 3-6 hours);

disuccinimidyl tartarate (DST) and sulfo-DST, which are amine reactivecross-linking reagents, cleavable by 0.015 M sodium periodate;

bis[2-(succinimidyloxycarbonyloxy)ethyl]sulfone (BSOCOES) andsulfo-BSOCOES, which are amine reactive cross-linking reagents,cleavable by base (pH 11.6);

1,4-di-[3′-(2′-pyridyldithio(propionamido))butane (DPDPB), apyridyldithiol crosslinker which is cleavable by thiol exchange orreduction;

N-[4-(p-azidosalicylamido)-butyl]-3′-(2′-pyridydithio)propionamide(APDP), a pyridyldithiol crosslinker which is cleavable by thiolexchange or reduction;

bis-[beta-4-(azidosalicylamido)ethyl]-disulfide, a photoreactivecrosslinker which is cleavable by thiol exchange or reduction;

N-succinimidyl-(4-azidophenyl)-1,3′dithiopropionate (SADP), aphotoreactive crosslinker which is cleavable by thiol exchange orreduction;

sulfosuccinimidyl-2-(7-azido-4-methylcoumarin-3-acetamide)ethyl-1,3′-dithiopropionate(SAED), a photoreactive crosslinker which is cleavable by thiol exchangeor reduction;

sulfosuccinimidyl-2-(m-azido-o-nitrobenzamido)-ethyl-1,3′dithiopropionate(SAND), a photoreactive crosslinker which is cleavable by thiol exchangeor reduction.

Other examples of cleavable linkers and the cleavage conditions that canbe used to release tags are as follows. A silyl linking group can becleaved by fluoride or under acidic conditions. A 3-, 4-, 5-, or6-substituted-2-nitrobenzyloxy or 2-, 3-, 5-, or6-substituted-4-nitrobenzyloxy linking group can be cleaved by a photonsource (photolysis). A 3-, 4-, 5-, or 6-substituted-2-alkoxyphenoxy or2-, 3-, 5-, or 6-substituted-4-alkoxyphenoxy linking group can becleaved by Ce(NH₄)₂(NO₃)₆ (oxidation). A NCO₂ (urethane) linker can becleaved by hydroxide (base), acid, or LiAlH₄ (reduction). A 3-pentenyl,2-butenyl, or 1-butenyl linking group can be cleaved by O₃, O_(S)O₄/IO₄⁻, or KMnO₄ (oxidation). A 2-[3-, 4-, or 5-substituted-furyl]oxy linkinggroup can be cleaved by O₂, Br₂, MeOH, or acid.

Conditions for the cleavage of other labile linking groups include:t-alkyloxy linking groups can be cleaved by acid; methyl(dialkyl)methoxyor 4-substitued-2-alkyl-1,3-dioxlane-2-yl linking groups can be cleavedby H₃O⁺; 2-silylethoxy linking groups can be cleaved by fluoride oracid; 2-(X)-ethoxy (where X=keto, ester amide, cyano, NO₂, sulfide,sulfoxide, sulfone) linking groups can be cleaved under alkalineconditions; 2-, 3-, 4-, 5-, or 6-substituted-benzyloxy linking groupscan be cleaved by acid or under reductive conditions; 2-butenyloxylinking groups can be cleaved by (Ph₃P)₃RhCl(H), 3-, 4-, 5-, or6-substituted-2-bromophenoxy linking groups can be cleaved by Li, Mg, orBuLi; methylthiomethoxy linking groups can be cleaved by Hg²⁺;2-(X)-ethyloxy (where X=a halogen) linking groups can be cleaved by Znor Mg; 2-hydroxyethyloxy linking groups can be cleaved by oxidation(e.g., with Pb(OAc)₄).

Preferred linkers are those that are cleaved by acid or photolysis.Several of the acid-labile linkers that have been developed for solidphase peptide synthesis are useful for linking tags to MOIs. Some ofthese linkers are described in a recent review by Lloyd-Williams et al.(Tetrahedron 49:11065-11133, 1993). One useful type of linker is basedupon p-alkoxybenzyl alcohols, of which two, 4-hydroxymethylphenoxyaceticacid and 4-(4-hydroxymethyl-3-methoxyphenoxy)butyric acid, arecommercially available from Advanced ChemTech (Louisville, Ky.). Bothlinkers can be attached to a tag via an ester linkage to thebenzylalcohol, and to an amine-containing MOI via an amide linkage tothe carboxylic acid. Tags linked by these molecules are released fromthe MOI with varying concentrations of trifluoroacetic acid. Thecleavage of these linkers results in the liberation of a carboxylic acidon the tag. Acid cleavage of tags attached through related linkers, suchas 2,4-dimethoxy-4′-(carboxymethyloxy)-benzhydrylamine (available fromAdvanced ChemTech in FMOC-protected form), results in liberation of acarboxylic amide on the released tag.

The photolabile linkers useful for this application have also been forthe most part developed for solid phase peptide synthesis (seeLloyd-Williams review). These linkers are usually based on2-nitrobenzylesters or 2-nitrobenzylamides. Two examples of photolabilelinkers that have recently been reported in the literature are4-(4-(1-Fmoc-amino)ethyl)-2-methoxy-5-nitrophenoxy)butanoic acid (Holmesand Jones, J. Org Chem. 60:2318-2319, 1995) and3-(Fmoc-amino)-3-(2-nitrophenyl)propionic acid (Brown et al., MolecularDiversity 1:4-12, 1995). Both linkers can be attached via the carboxylicacid to an amine on the MOI. The attachment of the tag to the linker ismade by forming an amide between a carboxylic acid on the tag and theamine on the linker. Cleavage of photolabile linkers is usuallyperformed with UV light of 350 nm wavelength at intensities and timesknown to those in the art. Cleavage of the linkers results in liberationof a primary amide on the tag. Examples of photocleavable linkersinclude nitrophenyl glycine esters, exo- and endo-2-benzonorborneylchlorides and methane sulfonates, and 3-amino-3(2-nitrophenyl) propionicacid. Examples of enzymatic cleavage include esterases which will cleaveester bonds, nucleases which will cleave phosphodiester bonds, proteaseswhich cleave peptide bonds, etc.

A preferred linker component has an ortho-nitrobenzyl structure as shownbelow:

wherein one carbon atom at positions a, b, c, d or e is substituted with—L³—X, and L¹ (which is preferably a direct bond) is present to the leftof N(R¹) in the above structure. Such a linker component is susceptibleto selective photo-induced cleavage of the bond between the carbonlabeled “a” and N(R¹). The identity of R¹ is not typically critical tothe cleavage reaction, however R¹ is preferably selected from hydrogenand hydrocarbyl. The present invention provides that in the abovestructure, —N(R¹)— could be replaced with —O—. Also in the abovestructure, one or more of positions b, c, d or e may optionally besubstituted with alkyl, alkoxy, fluoride, chloride, hydroxyl,carboxylate or amide, where these substituents are independentlyselected at each occurrence.

A further preferred linker component with a chemical handle L_(h) hasthe following structure:

wherein one or more of positions b, c, d or e is substituted withhydrogen, alkyl, alkoxy, fluoride, chloride, hydroxyl, carboxylate oramide, R¹ is hydrogen or hydrocarbyl, and R² is —OH or a group thateither protects or activates a carboxylic acid for coupling with anothermoiety. Fluorocarbon and hydrofluorocarbon groups are preferred groupsthat activate a carboxylic acid toward coupling with another moiety.

3. Molecule of Interest (MOI)

Examples of MOIs include nucleic acids or nucleic acid analogues (e.g.,PNA), fragments of nucleic acids (i.e., nucleic acid fragments),synthetic nucleic acids or fragments, oligonucleotides (e.g., DNA orRNA), proteins, peptides, antibodies or antibody fragments, receptors,receptor ligands, members of a ligand pair, cytokines, hormones,oligosaccharides, synthetic organic molecules, drugs, and combinationsthereof.

Preferred MOIs include nucleic acid fragments. Preferred nucleic acidfragments are primer sequences that are complementary to sequencespresent in vectors, where the vectors are used for base sequencing.Preferably a nucleic acid fragment is attached directly or indirectly toa tag at other than the 3′ end of the fragment; and most preferably atthe 5′ end of the fragment. Nucleic acid fragments may be purchased orprepared based upon genetic databases (e.g., Dib et al., Nature380:152-154, 1996 and CEPH Genotype Database, http://www.cephb.fr) andcommercial vendors (e.g., Promega, Madison, Wis.).

As used herein, MOI includes derivatives of an MOI that containfunctionality useful in joining the MOI to a T—L—L_(h) compound. Forexample, a nucleic acid fragment that has a phosphodiester at the 5′end, where the phosphodiester is also bonded to an alkyleneamine, is anMOI. Such an MOI is described in, e.g., U.S. Pat. No. 4,762,779 which isincorporated herein by reference. A nucleic acid fragment with aninternal modification is also an MOI. An exemplary internal modificationof a nucleic acid fragment is where the base (e.g., adenine, guanine,cytosine, thymidine, uracil) has been modified to add a reactivefunctional group. Such internally modified nucleic acid fragments arecommercially available from, e.g., Glen Research, Herndon, Va. Anotherexemplary internal modification of a nucleic acid fragment is where anabasic phosphoramidate is used to synthesize a modified phosphodiesterwhich is interposed between a sugar and phosphate group of a nucleicacid fragment. The abasic phosphoramidate contains a reactive groupwhich allows a nucleic acid fragment that contains thisphosphoramidate-derived moiety to be joined to another moiety, e.g., aT—L—L_(h) compound. Such abasic phosphoramidates are commerciallyavailable from, e.g., Clonetech Laboratories, Inc., Palo Alto, Calif.

4. Chemical Handles (L_(h))

A chemical handle is a stable yet reactive atomic arrangement present aspart of a first molecule, where the handle can undergo chemical reactionwith a complementary chemical handle present as part of a secondmolecule, so as to form a covalent bond between the two molecules. Forexample, the chemical handle may be a hydroxyl group, and thecomplementary chemical handle may be a carboxylic acid group (or anactivated derivative thereof, e.g., a hydrofluroaryl ester), whereuponreaction between these two handles forms a covalent bond (specifically,an ester group) that joins the two molecules together.

Chemical handles may be used in a large number of covalent bond-formingreactions that are suitable for attaching tags to linkers, and linkersto MOIs. Such reactions include alkylation (e.g., to form ethers,thioethers), acylation (e.g., to form esters, amides, carbamates, ureas,thioureas), phosphorylation (e.g., to form phosphates, phosphonates,phosphoramides, phosphonamides), sulfonylation (e.g., to formsulfonates, sulfonamides), condensation (e.g., to form imines, oximes,hydrazones), silylation, disulfide formation, and generation of reactiveintermediates, such as nitrenes or carbenes, by photolysis. In general,handles and bond-forming reactions which are suitable for attaching tagsto linkers are also suitable for attaching linkers to MOIs, andvice-versa. In some cases, the MOI may undergo prior modification orderivitization to provide the handle needed for attaching the linker.

One type of bond especially useful for attaching linkers to MOIs is thedisulfide bond. Its formation requires the presence of a thiol group(“handle”) on the linker, and another thiol group on the MOI. Mildoxidizing conditions then suffice to bond the two thiols together as adisulfide. Disulfide formation can also be induced by using an excess ofan appropriate disulfide exchange reagent, e.g., pyridyl disulfides.Because disulfide formation is readily reversible, the disulfide mayalso be used as the cleavable bond for liberating the tag, if desired.This is typically accomplished under similarly mild conditions, using anexcess of an appropriate thiol exchange reagent, e.g., dithiothreitol.

Of particular interest for linking tags (or tags with linkers) tooligonucleotides is the formation of amide bonds. Primary aliphaticamine handles can be readily introduced onto synthetic oligonucleotideswith phosphoramidites such as6-monomethoxytritylhexylcyanoethyl-N,N-diisopropyl phosphoramidite(available from Glenn Research, Sterling, Va.). The amines found onnatural nucleotides such as adenosine and guanosine are virtuallyunreactive when compared to the introduced primary amine. Thisdifference in reactivity forms the basis of the ability to selectivelyform amides and related bonding groups (e.g., ureas, thioureas,sulfonamides) with the introduced primary amine, and not the nucleotideamines.

As listed in the Molecular Probes catalog (Eugene, Oreg.), a partialenumeration of amine-reactive functional groups includes activatedcarboxylic esters, isocyanates, isothiocyanates, sulfonyl halides, anddichlorotriazenes. Active esters are excellent reagents for aminemodification since the amide products formed are very stable. Also,these reagents have good reactivity with aliphatic amines and lowreactivity with the nucleotide amines of oligonucleotides. Examples ofactive esters include N-hydroxysuccinimide esters, pentafluorophenylesters, tetrafluorophenyl esters, and p-nitrophenyl esters. Activeesters are useful because they can be made from virtually any moleculethat contains a carboxylic acid. Methods to make active esters arelisted in Bodansky (Principles of Peptide Chemistry (2d ed.), SpringerVerlag, London, 1993).

5. Linker Attachment

Typically, a single type of linker is used to connect a particular setor family of tags to a particular set or family of MOIs. In a preferredembodiment of the invention, a single, uniform procedure may be followedto create all the various T—L—MOI structures. This is especiallyadvantageous when the set of T—L—MOI structures is large, because itallows the set to be prepared using the methods of combinatorialchemistry or other parallel processing technology. In a similar manner,the use of a single type of linker allows a single, uniform procedure tobe employed for cleaving all the various T—L—MOI structures. Again, thisis advantageous for a large set of T—L—MOI structures, because the setmay be processed in a parallel, repetitive, and/or automated manner.

There are, however, other embodiment of the present invention, whereintwo or more types of linker are used to connect different subsets oftags to corresponding subsets of MOIs. In this case, selective cleavageconditions may be used to cleave each of the linkers independently,without cleaving the linkers present on other subsets of MOIs.

A large number of covalent bond-forming reactions are suitable forattaching tags to linkers, and linkers to MOIs. Such reactions includealkylation (e.g., to form ethers, thioethers), acylation (e.g., to formesters, amides, carbamates, ureas, thioureas), phosphorylation (e.g., toform phosphates, phosphonates, phosphoramides, phosphonamides),sulfonylation (e.g., to form sulfonates, sulfonamides), condensation(e.g., to form imines, oximes, hydrazones), silylation, disulfideformation, and generation of reactive intermediates, such as nitrenes orcarbenes, by photolysis. In general, handles and bond-forming reactionswhich are suitable for attaching tags to linkers are also suitable forattaching linkers to MOIs, and vice-versa. In some cases, the MOI mayundergo prior modification or derivitization to provide the handleneeded for attaching the linker.

One type of bond especially useful for attaching linkers to MOIs is thedisulfide bond. Its formation requires the presence of a thiol group(“handle”) on the linker, and another thiol group on the MOI. Mildoxidizing conditions then suffice to bond the two thiols together as adisulfide. Disulfide formation can also be induced by using an excess ofan appropriate disulfide exchange reagent, e.g., pyridyl disulfides.Because disulfide formation is readily reversible, the disulfide mayalso be used as the cleavable bond for liberating the tag, if desired.This is typically accomplished under similarly mild conditions, using anexcess of an appropriate thiol exchange reagent, e g., dithiothreitol.

Of particular interest for linking tags to oligonucleotides is theformation of amide bonds. Primary aliphatic amine handles can be readilyintroduced onto synthetic oligonucleotides with phosphoramidites such as6-monomethoxytritylhexyclcyanoethyl-N,N-diisopropyl phosphoramidite(available from Glenn Research, Sterling, Va.). The amines found onnatural nucleotides such as adenosine and guanosine are virtuallyunreactive when compared to the introduced primary amine. Thisdifference in reactivity forms the basis of the ability to selectivelyform amides and related bonding groups (e.g., ureas, thioureas,sulfonamides) with the introduced primary amine, and not the nucleotideamines.

As listed in the Molecular Probes catalog (Eugene, Oreg.), a partialenumeration of amine-reactive functional groups includes activatedcarboxylic esters, isocyanates, isothiocyanates, sulfonyl halides, anddichlorotriazenes. Active esters are excellent reagents for aminemodification since the amide products formed are very stable. Also,these reagents have good reactivity with aliphatic amines and lowreactivity with the nucleotide amines of oligonucleotides. Examples ofactive esters include N-hydroxysuccinimide esters, pentafluorophenylesters, tetrafluorophenyl esters, and p-nitrophenyl esters. Activeesters are useful because they can be made from virtually any moleculethat contains a carboxylic acid. Methods to make active esters arelisted in Bodansky (Principles of Peptide Chemistry (2d ed.), SpringerVerlag, London, 1993).

Numerous commercial cross-linking reagents exist which can serve aslinkers (e.g., see Pierce Cross-linkers, Pierce Chemical Co., Rockford,Ill.). Among these are homobifunctional amine-reactive cross-linkingreagents which are exemplified by homobifunctional imidoesters andN-hydroxysuccinimidyl (NHS) esters. There also exist heterobifunctionalcross-linking reagents possess two or more different reactive groupsthat allows for sequential reactions. Imidoesters react rapidly withamines at alkaline pH. NHS-esters give stable products when reacted withprimary or secondary amines. Maleimides, alkyl and aryl halides,alpha-haloacyls and pyridyl disulfides are thiol reactive. Maleimidesare specific for thiol (sulfhydryl) groups in the pH range of 6.5 to7.5, and at alkaline pH can become amine reactive. The thioether linkageis stable under physiological conditions. Alpha-haloacetyl cross-linkingreagents contain the iodoacetyl group and are reactive towardssulfhydryls. Imidazoles can react with the iodoacetyl moiety, but thereaction is very slow. Pyridyl disulfides react with thiol groups toform a disulfide bond. Carbodiimides couple carboxyls to primary aminesof hydrazides which give rises to the formation of an acyl-hydrazinebond. The arylazides are photoaffinity reagents which are chemicallyinert until exposed to UV or visible light. When such compounds arephotolyzed at 250-460 nm, a reactive aryl nitrene is formed. Thereactive aryl nitrene is relatively non-specific. Glyoxals are reactivetowards guanidinyl portion of arginine.

In one typical embodiment of the present invention, a tag is firstbonded to a linker, then the combination of tag and linker is bonded toa MOI, to create the structure T—L—MOI. Alternatively, the samestructure is formed by first bonding a linker to a MOI, and then bondingthe combination of linker and MOI to a tag. An example is where the MOIis a DNA primer or oligonucleotide. In that case, the tag is typicallyfirst bonded to a linker, then the T—L is bonded to a DNA primer oroligonucleotide, which is then used, for example, in a sequencingreaction.

One useful form in which a tag could be reversibly attached to an MOI(e.g., an oligonucleotide or DNA sequencing primer) is through achemically labile linker. One preferred design for the linker allows thelinker to be cleaved when exposed to a volatile organic acid, forexample, trifluoroacetic acid (TFA). TFA in particular is compatiblewith most methods of MS ionization, including electrospray.

As described in detail below, the invention provides methodology forgenotyping. A composition which is useful in the genotyping methodcomprises a a plurality of compounds of the formula:

T^(ms)—L—MOI

wherein,

T^(ms) is an organic group detectable by mass spectrometry, comprisingcarbon, at least one of hydrogen and fluoride, and optional atomsselected from oxygen, nitrogen, sulfur, phosphorus and iodine. In theformula, L is an organic group which allows a T^(ms)-containing moietyto be cleaved from the remainder of the compound, wherein theT^(ms)-containing moiety comprises a functional group which supports asingle ionized charge state when the compound is subjected to massspectrometry and is selected from tertiary amine, quaternary amine andorganic acid. In the formula, MOI is a nucleic acid fragment wherein Lis conjugated to the MOI at a location other than the 3′ end of the MOI.In the composition, at least two compounds have the same T^(ms) but theMOI groups of those molecules have non-identical nucleotide lengths.

Another composition that is useful in the genotyping method comprises aplurality of compounds of the formula:

T^(ms)—L—MOI

wherein T^(ms) is an organic group detectable by mass spectrometry,comprising carbon, at least one of hydrogen and fluoride, and optionalatoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine. Inthe formula, L is an organic group which allows a T^(ms)-containingmoiety to be cleaved from the remainder of the compound, wherein theT^(ms)-containing moiety comprises a functional group which supports asingle ionized charge state when the compound is subjected to massspectrometry and is selected from tertiary amine, quaternary amine andorganic acid. In the formula, MOI is a nucleic acid fragment wherein Lis conjugated to the MOI at a location other than the 3′ end of the MOI.In the composition, at least two compounds have the same T^(ms) butthose compounds have non-identical elution times by columnchromatography.

Another composition that may be used in the genotyping method comprisesa plurality of compounds of the formula:

T^(ms)—L—MOI

wherein T^(ms) is an organic group detectable by mass spectrometry,comprising carbon, at least one of hydrogen and fluoride, and optionalatoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine. Inthe formula, L is an organic group which allows a T^(ms)-containingmoiety to be cleaved from the remainder of the compound, wherein theT^(ms)-containing moiety comprises a functional group which supports asingle ionized charge state when the compound is subjected to massspectrometry and is selected from tertiary amine, quaternary amine andorganic acid. In the formula, MOI is a nucleic acid fragment wherein Lis conjugated to the MOI at a location other than the 3′ end of the MOI.In the composition, no two compounds which have the same MOI nucleotidelength also have the same T^(ms).

In the above composition, the plurality is preferably greater than 2,and preferably greater than 4. Also, the nucleic acid fragment in theMOI have a sequence complementary to a portion of a vector, wherein thefragment is capable of priming polynucleotide synthesis. Preferably, theT^(ms) groups of members of the plurality differ by at least 2 amu, andmay differ by at least 4 amu.

The invention also provides for a composition comprising a plurality ofsets of compounds, each set of compounds having the formula:

T^(ms)—L—MOI

wherein T^(ms) is an organic group detectable by mass spectrometry,comprising carbon, at least one of hydrogen and fluoride, and optionalatoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine. Inthe formula, L is an organic group which allows a T^(ms)-containingmoiety to be cleaved from the remainder of the compound, wherein theT^(ms)-containing moiety comprises a functional group which supports asingle ionized charge state when the compound is subjected to massspectrometry and is selected from tertiary amine, quaternary amine andorganic acid. Also, in the formula, MOI is a nucleic acid fragmentwherein L is conjugated to the MOI at a location other than the 3′ endof the MOI. In the composition, members within a first set of compoundshave identical Tms groups, however have non-identical MOI groups withdiffering numbers of nucleotides in the MOI and there are at least tenmembers within the first set, wherein between sets, the T^(ms) groupsdiffer by at least 2 amu. The plurality is preferably at least 3, andmore preferably at least 5.

The invention also provides for a composition comprising a plurality ofsets of compounds, each set of compounds having the formula

T^(ms)—L—MOI

wherein, T^(ms) is an organic group detectable by mass spectrometry,comprising carbon, at least one of hydrogen and fluoride, and optionalatoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine. Inthe formula, L is an organic group which allows a T^(ms)-containingmoiety to be cleaved from the remainder of the compound, wherein theT^(ms)-containing moiety comprises a functional group which supports asingle ionized charge state when the compound is subjected to massspectrometry and is selected from tertiary amine, quaternary amine andorganic acid. In the formula, MOI is a nucleic acid fragment wherein Lis conjugated to the MOI at a location other than the 3′ end of the MOI.In the composition, the compounds within a set have the same elutiontime but non-identical T^(ms) groups.

In addition, the invention provides a kit for genotyping. The kitcomprises a plurality of amplification primer pairs, wherein at leastone of the primers has the formula:

T^(ms)—L—MOI

wherein T^(ms) is an organic group detectable by mass spectrometry,comprising carbon, at least one of hydrogen and fluoride, and optionalatoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine. Inthe formula, L is an organic group which allows a T^(ms)-containingmoiety to be cleaved from the remainder of the compound, wherein theT^(ms)-containing moiety comprises a functional group which supports asingle ionized charge state when the compound is subjected to massspectrometry and is selected from tertiary amine, quaternary amine andorganic acid. In the formula, MOI is a nucleic acid fragment wherein Lis conjugated to the MOI at a location other than the 3′ end of the MOI;and each primer pair associates with a different loci. In the kit, theplurality is preferably at least 3, and more preferably at least 5.

As noted above, the present invention provides compositions and methodsfor determining the sequence of nucleic acid molecules. Briefly, suchmethods generally comprise the steps of (a) generating tagged nucleicacid fragments which are complementary to a selected nucleic acidmolecule (e.g., tagged fragments) from a first terminus to a secondterminus of a nucleic acid molecule), wherein a tag is correlative witha particular or selected nucleotide, and may be detected by any of avariety of methods, (b) separating the tagged fragments by sequentiallength, (c) cleaving a tag from a tagged fragment, and (d) detecting thetags, and thereby determining the sequence of the nucleic acid molecule.Each of the aspects will be discussed in more detail below.

B. Diagnostic Methods

1. Introduction

As noted above, the present invention also provides a wide variety ofmethods wherein the above-described tags and/or linkers may be utilizedin place of traditional labels (e.g., radioactive or enzymatic), inorder to enhance the specificity, sensitivity, or number of samples thatmay be simultaneously analyzed, within a given method. Representativeexamples of such methods which may be enhanced include, for example, RNAamplification (see Lizardi et al., Bio/Technology 6:1197-1202, 1988;Kramer et al., Nature 339:401-402, 1989; Lomeli et al., Clinical Chem.35(9):1826-1831, 1989; U.S. Pat. No. 4,786,600), and DNA amplificationutilizing LCR or polymerase chain reaction (“PCR”) (see, U.S. Pat. Nos.4,683,195, 4,683,202, and 4,800,159).

Within one aspect of the present invention, methods are provided fordetermining the identity of a nucleic acid molecule or fragment (or fordetecting the presence of a selected nucleic acid molecule or fragment),comprising the steps of (a) generating tagged nucleic acid moleculesfrom one or more selected target nucleic acid molecules, wherein a tagis correlative with a particular nucleic acid molecule and detectable bynon-fluorescent spectrometry or potentiometry, (b) separating the taggedmolecules by size, (c) cleaving the tags from the tagged molecules, and(d) detecting the tags by non-fluorescent spectrometry or potentiometry,and therefrom determining the identity of the nucleic acid molecules.

Within a related aspect of the invention, methods are provided fordetecting a selected nucleic acid molecule, comprising the steps of (a)combining tagged nucleic acid probes with target nucleic acid moleculesunder conditions and for a time sufficient to permit hybridization of atagged nucleic acid probe to a complementary selected target nucleicacid sequence, wherein a tagged nucleic acid probe is detectable bynon-fluroescent spectrometry or potentiometry, (b) altering the size ofhybridized tagged probes, unhybridized probes or target molecules, orthe probe:target hybrids, (c) separating the tagged probes by size, (d)cleaving tags from the tagged probes, and (e) detecting tags bynon-fluorescent spectrometry or potentiometry, and therefrom detectingthe selected nucleic acid molecule. These, other related techniques arediscussed in more detail below.

2. PCR

PCR can amplify a desired DNA sequence of any origin (virus, bacteria,plant, or human) hundreds of millions of times in a matter of hours. PCRis especially valuable because the reaction is highly specific, easilyautomated, and capable of amplifying minute amounts of sample. For thesereasons, PCR has had a major impact on clinical medicine, geneticdisease diagnostics, forensic science and evolutionary biology.

Briefly, PCR is a process based on a specialized polymerase, which cansynthesize a complementary strand to a given DNA strand in a mixturecontaining the 4 DNA bases and 2 DNA fragments (primers, each about 20bases long) flanking the target sequence. The mixture is heated toseparate the strands of double-stranded DNA containing the targetsequence and then cooled to allow (1) the primers to find and bind totheir complementary sequences on the separated strands and (2) thepolymerase to extend the primers into new complementary strands.Repeated heating and cooling cycles multiply the target DNAexponentially, since each new double strand separates to become twotemplates for further synthesis. In about 1 hour, 20 PCR cycles canamplify the target by a millionfold.

Within one embodiment of the invention, methods are provided fordetermining the identity of a nucleic acid molecule, or for detectingthe selected nucleic acid molecule in, for example, a biological sample,utilizing the technique of PCR. Briefly, such methods comprise the stepsof generating a series of tagged nucleic acid fragments or moleculesduring the PCR and separating the resulting fragments are by size. Thesize separation step can be accomplished utilizing any of the techniquesdescribed herein, including for example gel electrophoresis (e.g.,polyacrylamide gel electrophoresis) or preferably HPLC The tags are thencleaved from the separated fragments and detected by the respectivedetection technology. Examples of such technologies have been describedherein, and include for example mass spectrometry, infra-redspectrometry, potentiostatic amperometry or UV spectrometry.

3. RNA Fingerprinting and Differential Display

When the template is RNA, the first step in fingerprinting is reversetranscription. Liang and Pardee (Science 257:967, 1992) were the firstto describe an RNA fingerprinting protocol, using a primer for reversetranscription based on oligo (dT) but with an ‘anchor’ of two bases atthe 5′ end (e.g., oligo 5′-(dT₁₁)CA-3′. Priming occurs mainly at the 5′end of the poly(rA) tail and mainly in sequences that end5′-UpG-poly(rA)-3′, with a selectivity approaching one out of 12polyadenylated RNAs. After reverse transcription and denaturation,arbitrary priming is performed on the resulting first strand of cDNA.PCR can now be used to generate a fingerprint of products that bestmatches the primers and that are derived from the 3′ end of the mRNAsand polyadenylated heterogeneous RNAs. This protocol has been named‘differential display’.

Alternatively, an arbitrary primer can be used in the first step ofreverse transcription, selecting those regions internal to the RNA thathave 6-8 base matches with the 3′ end of the primer. This is followed byarbitrary priming of the resulting first strand of cDNA with the same ora different arbitrary primer and then PCR. This particular protocolsamples anywhere in the RNA, including open reading frames (Welsh etal., Nuc. Acids. Res. 20:4965, 1992). In addition, it can be used onRNAs that are not polyadenylated, such as many bacterial RNAs. Thisvariant of RNA fingerprinting by arbitrarily primed PCR has been calledRAP-PCR.

If arbitrarily primed PCR fingerprinting of RNA is performed on samplesderived from cells, tissues or other biological material that have beensubjected to different experimental treatments or have differentdevelopmental histories, differences in gene expression between thesamples can be detected. For each reaction, it is assumed that the samenumber of effective PCR doubling events occur and any differences in theinitial concentrations of cDNA products are preserved as a ratio ofintensities in the final fingerprint. There are no meaningfulrelationships between the intensities of bands within a single lane on agel, which are a function of match and abundance. However, the ratiobetween lanes is preserved for each sampled RNA, allowing differentiallyexpressed RNAs to be detected. The ratio of starting materials betweensamples is maintained even when the number of cycles is sufficient toallow the PCR reaction to saturate. This is because the number ofdoublings needed to reach saturation are almost completely controlled bythe invariant products that make up the majority of the fingerprint. Inthis regard, PCR fingerprinting is different from conventional PCR of asingle product in which the ratio of starting materials between samplesis not preserved unless products are sampled in the exponential phase ofamplification.

Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the technique of RNA fingerprinting. Briefly, such methodsgenerally comprise the steps of generating a series of tagged nucleicacid fragments. The fragments generated by PCR or similar amplificationschemes and are then subsequently separated by size. The size separationstep can be, for example, any of the techniques described herein,including for example gel electrophoresis (e.g., polyacrylamide gelelectrophoresis) or preferably HPLC. The tags are then cleaved from theseparated fragments, and then the tags are detected by the respectivedetection technology. Representative examples of suitable technologiesinclude mass spectrometry, infra-red spectrometry, potentiostaticamperometry or UV spectrometry. The relative quantities of any givennucleic acid fragments are not important, but the size of the band isinformative when referenced to a control sample.

4. Fluorescence-Based PCR Single-Strand Conformation Polymorphism(PCR-SSCP)

A number of methods in addition to the RFLP approach are available foranalyzing base substitution polymorphisms. Orita, et al. have devised away of analyzing these polymorphisms on the basis of conformationaldifferences in denatured DNA. Briefly, restriction enzyme digestion orPCR is used to produce relatively small DNA fragments which are thendenatured and resolved by electrophoresis on non-denaturingpolyacrylamide gels. Conformational differences in the single-strandedDNA fragments resulting from base substitutions are detected byelectrophoretic mobility shifts. Intra-strand base pairing createssingle strand conformations that are highly sequence-specific anddistinctive in electrophoretic mobility. However, detection rates indifferent studies using conventional SSCP range from 35% to nearly 100%with the highest detection rates most often requiring several differentconditions. In principle, the method could also be used to analyzepolymorphisms based on short insertions or deletions. This method is oneof the most powerful tools for identifying point mutations and deletionsin DNA (SSCP-PCR, Dean et al., Cell 61:863, 1990).

Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the technique of PCR-SSP. Briefly, such methods generallycomprise the steps of generating a series of tagged nucleic acidfragments. The fragments generated by PCR are then separated by size.Preferably, the size separation step is non-denaturing and the nucleicacid fragments are denatured prior to the separation methodology. Thesize separation step can be accomplished, for example gelelectrophoresis (e.g., polyacrylamide gel electrophoresis) or preferablyHPLC. The tags are then cleaved from the separated fragments, and thenthe tags are detected by the respective detection technology (e.g., massspectrometry, infra-red spectrometry, potentiostatic amperometry or UVspectrometry).

5. Dideoxy Fingerprinting (ddF)

Another method has been described (ddF, Sarkar et al., Genomics 13:441,1992) that detected 100% of single-base changes in the human factor IXgene when tested in a retrospective and prospective manner. In total, 84of 84 different sequence changes were detected when genomic DNA wasanalyzed from patients with hemophilia B.

Briefly, in the applications of tags for genotyping or other purposes,one method that can be used is dideoxy-fingerprinting. This methodutilizes a dideoxy terminator in a Sanger sequencing reation. Theprinciple of the method is as follows: a target nucleic acid that is tobe sequenced is placed in a reaction which possesses adideoxy-terminator complementary to the base known to be mutated in thetarget nucleic acid. For example, if the mutation results in a A→Gchange, the reaction would be carried out in a C dideoxy-terminatorreaction. PCR primers are used to locate and amplify the target sequenceof interest. If the hypothetical target sequence contains the A→Gchange, the size of a population of sequences is changed due to theincorporation of a dideoxy-terminator in the amplified sequences. Inthis particular application of tags, a fragment would be generated whichwould possess a predictable size in the case of a mutation. The tagswould be attached to the 5′-end of the PCR primers and provide a “map”to sample type and dideoxy-terminator type. A PCR amplification reactionwould take place, the resulting fragments would be separated by size byfor example HPLC or PAGE. At the end of the separation procedure, theDNA fragments are collected in a temporal reference frame, the tags arecleaved and the presence or absence of mutation is determined by thechain length due to premature chain terminator by the incorporation of agiven dideoxy-terminator.

It is important to note that ddf results in the gain or loss of adideoxy-termination segment and or a shift in the mobility of at leastone of the termination segments or products. Therefore, in this method,a search is made of the shift of one fragment mobility in a highbackground of other molecular weight fragments. One advantage is theforeknowledge of the length of fragment associated with a givenmutation.

Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the technique of ddF. Briefly, such methods generally comprisethe steps of generating a series of tagged nucleic acid fragments,followed by separation based upon size. Preferably, the size separationstep is non-denaturing and the nucleic acid fragments are denaturedprior to the separation methodology. The size separation step can beaccomplished, for example gel electrophoresis (e.g., polyacrylamide gelelectrophoresis) or preferably HPLC. The tags are then cleaved from theseparated fragments, and then the tags are detected by the respectivedetection technology (e.g., mass spectrometry, infra-red spectrometry,potentiostatic amperometry or UV spectrometry).

6. Restriction Maps and RFLPs

Restriction endonucleases recognize short DNA sequences and cut DNAmolecules at those specific sites. Some restriction enzymes(rare-cutters) cut DNA very infrequently, generating a small number ofvery large fragments (several thousand to a million bp). Most enzymescut DNA more frequently, thus generating a large number of smallfragments (less than a hundred to more than a thousand bp). On average,restriction enzymes with 4-base recognition sites will yield pieces 256bases long, 6-base recognition sites will yield pieces 4000 bases long,and 8-base recognition sites will yield pieces 64,000 bases long. Sincehundreds of different restriction enzymes have been characterized, DNAcan be cut into many different small fragments.

A wide variety of techniques have been developed for the analysis of DNApolymorphisms. The most widely used method, the restriction fragmentlength polymorphism (RFPL) approach, combines restriction enzymedigestion, gel electrophoresis, blotting to a membrane and hybridizationto a cloned DNA probe. Polymorphisms are detected as variations in thelengths of the labeled fragments on the blots. The RFLP approach can beused to analyze base substitutions when the sequence change falls withina restriction enzyme site or to analyze minisatellites/VNTRs by choosingrestriction enzymes that cut outside the repeat units. The agarose gelsdo not usually afford the resolution necessary to distinguishminisatellite/VNTR alleles differing by a single repeat unit, but manyof the minisatellite/VNTRs are so variable that highly informativemarkers can still be obtained.

Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the technique of restriction mapping or RFLPs. Briefly, suchmethods generally comprise the steps of generating a series of taggednucleic acid fragments in which the fragments generated are digestedwith restriction enzymes. The tagged fragments are generated byconducting a hybridization step of the tagged probes with the digestedtarget nucleic acid. The hybridization step can take place prior to orafter the restriction nuclease digestion. The resulting digested nucleicacid fragments are then separated by size. The size separation step canbe accomplished, for example gel electrophoresis (e.g., polyacrylamidegel electrophoresis) or preferably HPLC. The tags are then cleaved fromthe separated fragments, and then the tags are detected by therespective detection technology (e.g., mass spectrometry, infra-redspectrometry, potentiostatic amperometry or UV spectrometry).

7. DNA Fingerprinting

DNA fingerprinting involves the display of a set of DNA fragments from aspecific DNA sample. A variety of DNA fingerprinting techniques arepresently available (Jeffreys et al., Nature 314:67-73, 1985; Zabeau andVos, 1992); “Selective Restriction Fragment Amplification: A GeneralMethod for DNA Fingerprinting,” European Patent Application 92402629.7.;Vos et al., “DNA FINGERPRINTING. A New Technique for DNAFingerprinting.” Nucl. Acids Res. 23: 4407-4414, 1996; Bates, S. R. E.,Knorr, D. A., Weller, J. W., and Ziegle, J. S., “Instrumentation forAutomated Molecular Marker Acquisition and Analysis.” Chapter 14, pp.239-255, in The Impact of Plant Molecular Genetics, edited by B. W. S.Sobral, published by Birkhauser, 1996.

Thus, one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the technique of DNA fingerprinting. Briefly, such methodsgenerally comprise the steps of generating a series of tagged nucleicacid fragments, followed by separation of the fragments by size. Thesize separation step can be accomplished, for example gelelectrophoresis (e.g., polyacrylamide gel electrophoresis) or preferablyHPLC. The tags are then cleaved from the separated fragments, and thenthe tags are detected by the respective detection technology (e.g., massspectrometry, infra-red spectrometry, potentiostatic amperometry or UVspectrometry).

Briefly, DNA fingerprinting is based on the selective PCR amplificationof restriction fragments from a total digest of genomic DNA. Thetechnique involves three steps: 1) restriction of the DNA fragments andsubsequent ligation of oligonucleotide adaptors, 2) selectiveamplification of sets of restriction fragments, 3) gel analysis of theamplified fragments. PCR amplification of the restriction fragments isachieved by using the adaptor and restriction site sequence as targetsites for primer annealing. The selective amplification is achieved bythe use of primers that extend into the restriction fragments,amplifying only those fragments in which the primer extensions match thenucleotides flanking the restriction sites.

This method therefore yields sets of restriction fragments which may bevisualized by a variety of methods (i.e., PAGE, HPLC, or other types ofspectrometry) without prior knowledge of the nucleotide sequence. Themethod also allows the co-amplification of large numbers of restrictionfragments. The number of fragments however is dependent on theresolution of the detection system. Typically, 50-100 restrictionfragments are amplified and detected on denaturing polyacrylamide gels.In the application described herein, the separation will be performed byHPLC.

The DNA fingerprinting technique is based on the amplification ofsubsets of genomic restriction fragments using PCR. DNA is cut withrestriction enzymes and double strand adapters and the are ligated tothe ends of the DNA fragments to generate template DNA for theamplification reactions. The sequence of the ligated adapters and theadjacent restriction enzymes (sites) serve as binding sites for the DNAfingerprinting of primers for PCR-based amplification. Selectivenucleotides are included at the 3′ end of the of the PCR primers whichtherefore can only prime DNA synthesis from a subset of the restrictionsites. Only restriction fragments in which the nucleotides flanking therestriction site can match the selective nucleotide will be amplified.

The DNA fingerprinting process produces “fingerprint” patterns ofdifferent fragment lengths that are characteristic and reproducible foran individual organism. These fingerprints can be use to distinguisheven very closely related organisms, including near-isogenic lines. Thedifferences in fragment lengths can be traced to base changes in therestriction site or the primer extension site, or to insertions ordeletions in the body of the DNA fragment.

Dependence on sequence knowledge of the target genome is eliminated bythe use of adaptors of known sequence that are ligated to therestriction fragments. The PCR primers are specific for the knownsequences of the adaptors and restriction sites. The steps of thegenetic fingerprinting process are described below.

1) Restriction and Ligation. Restriction fragments of genomic DNA aregenerated by using two different restriction enzymes: a rare cutter (thesix-base recognition enzyme EcoRI) and a frequent cutter (the four-baserecognition enzyme MseI). Three different types of fragments areproduced: ones with EcoRI cuts at both ends, ones with MseI cuts at bothends, and ones with an EcoRI cut at one end and an MseI cut at the otherend. Double-stranded adaptors are then ligated to the sticky ends of theDNA fragments, generating template DNA for amplification. The adaptorsare specific for either the EcoRI site or the MseI site. Restriction andligation take place in a single reaction. Ligation of the adaptor to therestricted DNA alters the restriction site so as to prevent a secondrestriction from taking place after ligation has occurred.

2) Preselective Amplification. The sequences of the adaptors andrestriction sites serve as primer binding sites for the “preselectivePCR amplification.” The preselective primers each have a “selective”nucleotide that will recognize the subset of restriction fragmentshaving the matching nucleotide downstream from the restriction site. Theprimary products of the preselective PCR are those fragments having oneMseI cut and one EcoRI cut, and also having the matching internalnucleotide. The preselective amplification achieves a 16-fold reductionof the complexity of the fragment mixture.

3) Selective Amplification with CMST-Labeled Primers. The complexity ofthe PCR product mixture is further reduced (256-fold) and fragments arelabeled with a set of CMSTs by carrying out a second PCR using selectiveprimers labeled with CMSTs. It is possible to choose from among 64different primer pairs (resulting from all possible combinations ofeight MseI and eight EcoRI primers) for this amplification. Each ofthese primers possesses three selective nucleotides. The first is thesame as that used in the pre-selective amplification; the others can beany of the 16 possible combinations of the four nucleotides. Only thatsubset of fragments having matching nucleotides at all three positionswill be amplified at this stage in the amplification.

8. Application of Cleavable Tags to Genotyping and PolymorphismDetection

a. Introduction

Although a few known human DNA polymorphisms are based upon insertions,deletions or other rearrangements of non-repeated sequences, the vastmajority are based either upon single base substitutions or uponvariations in the number of tandem repeats. Base substitutions are veryabundant in the human genome, occurring on average once every 200-500bp. Length variations in blocks of tandem repeats are also common in thegenome, with at least tens of thousands of interspersed polymorphicsites (termed loci). Repeat lengths for tandem repeat polymorphismsrange from 1 bp in (dA)_(n)(dT)_(n) sequences to at least 170 bp inα-satellite DNA. Tandem repeat polymorphisms can be divided into twomajor groups which consist of minisatellites/variable number of tandemrepeats (VNTRs), with typical repeat lengths of tens of base pairs andwith tens to thousands of total repeat units, and microsatellites, withrepeat lengths of up to 6 bp and with maximum total lengths of about 70bp. Most of the microsatellite polymorphisms identified to date havebeen based on (dC-dA)_(n) or (dG-dT)_(n) dinucleotide repeat sequences.Analysis of microsatellite polymorphisms involves amplification by thepolymerase chain reaction (PCR) of a small fragment of DNA containing ablock of repeats followed by electrophoresis of the amplified DNA ondenaturing polyacrylamide gel. The PCR primers are complementary tounique sequences that flank the blocks of repeats. Polyacrylamide gels,rather than agarose gels, are traditionally used for microsatellitesbecause the alleles often only differ in size by a single repeat.

Thus, within one aspect of the present invention methods are providedfor genotyping a selected organism, comprising the steps of (a)generating tagged nucleic acid molecules from a selected targetmolecule, wherein a tag is correlative with a particular fragment andmay be detected by non-fluorescent spectrometry or potentiometry, (b)separating the tagged molecules by sequential length, (c) cleaving thetag from the tagged molecule, and (d) detecting the tag by nonfluorescent spectrometry or potentiometry, and therefrom determining thegenotype of the organism.

Within another aspect, methods are provided for genotyping a selectedorganism, comprising the steps of (a) combining a tagged nucleic acidmolecule with a selected target molecule under conditions and for a timesufficient to permit hybridization of the tagged molecule to the targetmolecule, wherein a tag is correlative with a particular fragment andmay be detected by non-fluorescent spectrometry or potentiometry, (b)separating the tagged fragments by sequential length, (c) cleaving thetag from the tagged fragment, and (d) detecting the tag bynon-fluorescent spectrometry or potentiometry, and therefrom determiningthe genotype of the organism.

b. Application of Cleavable Tags to Genotyping

A PCR approach to identify restriction fragment length polymorphism(RFPL) combines gel electrophoresis and detection of tags assoicatedwith specific PCR primers. In general, one PCR primer will possess onespecific tag. The tag will therefore represent one set of PCR primersand therefore a pre-determined DNA fragment length. Polymorphisms aredetected as variations in the lengths of the labeled fragments in a gelor eluting from a gel. Polyacrylamide gel electrophoresis will usuallyafford the resolution necessary to distinguish minisatellite/VNTRalleles differing by a single repeat unit. Analysis of microsatellitepolymorphisms involves amplification by the polymerase chain reaction(PCR) of a small fragment of DNA containing a block of repeats followedby electrophoresis of the amplified DNA on denaturing polyacrylamide gelor followed by separation of DNA fragments by HPLC. The amplified DNAwill be labeled using primers that have cleavable tags at the 5′ end ofthe primer. The primers are incorporated into the newly synthesizedstrands by chain extension. The PCR primers are complementary to uniquesequences that flank the blocks of repeats. Minisatellite/VNTRpolymorphisms can also be amplified, much as with the microsatellitesdescribed above.

Descriptions of many types of DNA sequence polymorphisms have providedthe fundamental basis for the understanding of the structure of thehuman genome (Botstein et al., Am. J. Human Genetics 32:p314, 1980;Donis-Keller, Cell 51:319, 1981; Weissenbach et al., Nature 359:794).The construction of extensive framework linkage maps has beenfacilitated by the use of these DNA polymorphisms and has provided apractical means for localization of disease genes by linkage.Microsatellite dinucleotide markers are proving to be very powerfultools in the identification of human genes which have been shown tocontain mutations and in some instances cause disease. Genomicdinucleotide repeats are highly polymorphic (Weber, 1990, GenomicAnalysis, Vol 1, pp 159-181, Cold Spring Laboratory Press, Cold SpringHarbor, N.Y.; Weber and Wong, 1993, Hum. Mol. Genetics, 2, p1123) andmay possess up to 24 alleles. Microsatellite dinucleotide repeats can beamplified using primers complementary to the unique regions surroundingthe dinucleotide repeat by PCR. Following amplification, severalamplified loci and be combined (multiplexed) prior to a size separationstep. The process of applying the amplified microsatellite fragments toa size separation step and then identifying the size and therefore theallele is known as genotyping. Chromosome specific markers which permita high level of multiplexing have been reported for performing wholegenome scans for linkage analysis (Davies et al., 1994, Nature, 371,p130).

Tags can be used to great effect in genotyping with microsatellites.Briefly, the PCR primers are constructed to carry tags and used in acarefully chosen PC reaction to amplify di-, tri-, or tetra-nucleotiderepeats. The amplification products are then separated according to sizeby methods such as HPLC or PAGE. The DNA fragments are then collected ina temporal fashion, the tags cleaved from their respective DNA fragmentsand length deduced from comparison to internal standards in the sizeseparation step. Allele identification is made from reference to size ofthe amplified products.

With cleavable tags approach to genotyping, it is possible to combinemultiple samples on a single separation step. There are two general waysin which this can performed. The first general method for highthrough-put screening is the detection of a single polymorphism in alarge group of individuals. In this senario a single or nested set ofPCR primers is used and each amplification is done with one DNA sampletype per reaction. The number of samples that can be combined in theseparation step is proportional to the number of cleavable tags that canbe generated per detection technology (i.e., 400-600 for massspectrometer tags). It is therefore possible to identify 1 to severalpolymorphisms in a large group of individuals simultaneously. The secondapproach is to use multiple sets of PCR primers which can identifynumerous polymorphisms on a single DNA sample (genotyping an individualfor example). In this approach PCR primers are combined in a singleamplification reaction which generate PCR products of different length.Each primer pair or nested set is encoded by a specific cleavable Tagwhich implies each PCR fragment will be encoded with a specific tag. Thereaction is run on a single separation step (see below). The number ofsamples that can be combined in the separation step is proportional tothe number of cleavable tags that can be generated per detectiontechnology (i.e., 400-600 for mass spectrometer tags).

c. Enzymatic Detection of Mutation and the Applications of Tags

In this particular application or method, mismatches in heteroduplexesare detected by enzymatic cleavage of mismatched base pairs in a givennucleic acid duplex. DNA sequences to be tested for the presence of amutation are amplified by PCR using a specific set of primers, theamplified products are denatured and mixed with denatured referencefragments and hybridized which result in the formation ofheteroduplexes. The heteroduplexes are then treated with enzymes whichrecognize and cleave the duplex if a mismatch is present. Such enzymesare nuclease S1, Mung bean nuclease, “resolvases”, T4 endonuclease IV,etc. Essentially any enzyme can be used which recognizes mismatches invitro and cleave the resulting mismatch. The treatment with theappropriate enzyme, the DNA duplexes are separated by size, by, forexample HPLC or PAGE. The DNA fragments are collected temporally. Tagsare cleaved and detected. The presence of a mutation is detected by theshift in mobility of a fragments relative to a wild-type referencefragment.

d. Applications of Tags to the Oligonucleotide Ligation Assay (OLA)

The oligonucleotide ligation assay as originally described by Landegrenet al. (Landegen et al., Science 241:487, 1988) is a useful techniquefor the identification of sequences (known) in very large and complexgenomes. The principle of the OLA reaction is based on the ability ofligase to covalently join two diagnostic oligonucleotides as theyhybridize adjacent to one another on a given DNA target. If thesequences at the probe junctions are not perfectly based-paired, theprobes will not be joined by the ligase. The ability of a thermostableligase to discriminate potential single base-pair differences whenpositioned at the 3′ end of the “upstream” probe provides theopportunity for single base-pair resolution (Barony, PNAS USA 88:189,1991). In the application of tags, the tags can be attached to a probewhich is ligated to the amplified product. After completion of the OLR,the fragments are separated on the basis of size, the tags cleaved anddetected by mass spectrometry.

e. Sequence Specific Amplification

PCR primers with a 3′ end complementary either to a mutant or normaloligonucleotide sequence can be used to selectively amplify one or theother allele (Newton et al., Nuc. Acids Res., 17, p2503; et al., 1989,Genomics, 5, p535; Okayama et al., 1989, J. Lab. Clin. Med., 114, p105;Sommer et al., 1989, Mayo Clin.Proc., 64, 1361; Wu et al., PNAS USA, 86,p2757). Usually the PCR products are visualized after amplification byPAGE, but the principle of sequence specific amplification can beapplied to solid phase formats.

f. Application of Tags to Some Amplification Based Assays

Genotyping of viruses: One application of tags is the genotyping oridentification of viruses by hybridization with tagged probes. Forexample, F+ RNA coliphages may be useful candidates as indicators forenteric virus contamination. Genotyping by nucleic acid hybridizationmethods is a reliable, rapid, simple, and inexpensive alternative toserotyping (Kafatos et. al., Nucleic Acids Res. 7:1541, 1979).Amplification techniques and nucleic aid hybridization techniques havebeen successfully used to classify a variety of microorganisms includingE. coli (Feng, Mol. Cell Probes 7:151, 1993). Representative examples ofviruses that may be detected utilizing the present invention includerotavirus (Sethabutr et. al., J. Med Virol. 37:192, 1992), hepatitisviruses such as hepatitis C virus (Stuyver et. al., J. Gen Virol.74:1093, 1993), herpes simplex virus (Matsumoto et. al., J. VirolMethods 40:119, 1992).

Prognostic applications of mutational analysis in cancers: Geneticalterations have been described in a variety of experimental mammalianand human neoplasms and represent the morphological basis for thesequence of morphological alterations observed in carcinogenesis(Vogelstein et al., NEJM 319:525, 1988). In recent years with the adventof molecular biology techniques, allelic losses on certain chromosomesor mutation of tumor suppressor genes as well as mutations in severaloncogenes (e.g., c-myc, c-jun, and the ras family) have been the moststudied entities. Previous work (Finkelstein et al., Arch Surg. 128:526,1993) has identified a correlation between specific types of pointmutations in the K-ras oncogene and the stage at diagnosis in colorectalcarcinoma. The results suggested that mutational analysis could provideimportant information of tumor aggressiveness, including the pattern andspread of metastasis. The prognostic value of TP53 and K-ras-2mutational analysis in stage III carconoma of the colon has morerecently been demonstrated (Pricolo et al., Am. J. Surg. 171:41, 1996).It is therefore apparent that genotyping of tumors and pre-cancerouscells, and specific mutation detection will become increasinglyimportant in the treatment of cancers in humans.

9. Single Nucleotide Extension Assay

The primer extension technique for the detection of single nucleotide ingenomic DNA was first described by Sokolov in 1989 (Nucleic Acids Res.18(12): 3671, 1989). In this paper, Sokolov described the singlenucleotide extension of 30-mers and 20-mers complementary to the knownsequence of the cystic fibrosis gene. It was shown that the method hadthe ability to correctly identify a single nucleotide change within tthe gene. The method was based on the use of radiolabelleddeoxynucleotides for a labeling method in the single nucleotideextension assay. Later publications described the use of singlenucleotide extension assays for genetic diseases such as hemophilia B(factor IX) and the cyctic fibrosis gene (Kuppuswamy et al., PNAS USA88:p1143-1147, 1991). Recently, the parameters of the single nucleotideextension assay in terms of the quantitative range, variability, andmultiplex analysis has been described in detail (Greenwood, A. D. andBurke, D. T., Genome Research 6:336-348, 1996).

The strategy is based on the fidelity of the DNA polymerase to add onlythe correctly paired nucleotide onto the 3′ end of the templatehybridized primer. Since only one dideoxy-terminator nucleotide is addedper reaction, it is a simple matter to sort out which primer has beenextended in all four types of dNTPs.

Hence, within one aspect of the invention methods are provided for thedetection of a single selected nucleic acid within a nucleic acidmolecule, comprising the steps of (a) hybridizing in at least twoseparate reactions a tagged primer and a target nucleic acid moleculeunder conditions and for a time sufficient to permit hybridization ofthe primer to the target nucleic acid molecule, wherein each reactioncontains an enzyme which will add a nucleotide chain terminator, and, anucleotide chain terminator complementary to adenosine, cytosine,guanosine, thymidine or uracil, and wherein each reaction contains adifferent nucleotide chain terminator, (b) separating tagged primers bysize, (c) cleaving the tag from the tagged primer, and (d) detecting thetag by non-fluorescent spectrometry or potentiometry, and therefromdetermining the presence of the selected nucleotide within the nucleicacid molecule.

As noted herein a wide variety of separation methods may be utilized,including for example liquid chromatographic means such as HPLC. Inaddition, a wide variety of detection methodologies may be utilized,including for example, mass spectrometry, infrared spectrometry,ultraviolet spectrometry, or, potentiostatic amperometry. Also, severaldifferent enzymes may be utilized (e.g., a polymerase), as well as anyof the tags provided herein. Within certain preferred embodiments, eachprimer which is utilized within a reaction has a different unique tag.In this manner, multiple samples (or multiple sites) may besimulataneously probed for the presence of selected nucleotides.

Single nucleotide assays such as those described herein may be utilizedto detect polymorphic variants, or to interrogate a biological samplefor the presence a specific nucleotide within or near a known sequence.Target nucleic acid molecules include not only DNA (e.g., genomic DNA),but RNA as well.

In general, this method involves hybridizing a primer to the target DNAsequence such that the 3′ end of the primer is immediately adjacent tothe mutation to be detected and identified. The procedure is similar tothe Sanger sequencing reaction except that only the dideoxynucleotide ofa given nucleotide is added to the reaction mixture. Eachdideoxynucleotide is labeled with a unique tag. Of the four reactionmixtures, solely one will add a dideoxyterminator on to the primersequence. If the mutation is present, it will be detected through theunique tag on the dideoxynucleotide and its identity established.Multiple mutations can be ascertained simultaneously by tagging the DNAprimer with a unique tag as well. Within one aspect of the inventionmethods are provided for analyzing single nucleotide mutations from aselected biological sample, comprising the steps of exposing nucleicacids from a biological sample and combining the exposed nucleic acidswith one or more selected nucleic acid probes, which may or may not betagged, under conditions and for a time sufficient for said probes tohybridize to said nucleic acids, wherein the tag, if used, iscorrelative with a particular nucleic acid probe and detectable bynon-fluorescent spectrometry, or potentiometry. The DNA fragments arereacted in four separate reactions each including a different taggeddideoxyterminator, wherein the tag is correlative with a particulardideoxynucleotide and detectable by non-fluorescent spectrometry, orpotentiometry. The DNA fragments are separated according to size by, forexample, gel electrophoresis (e.g., polyacrylamide gel electrophoresis)or preferably HPLC. The tags are cleaved from the separated fragmentsand detected by the respective detection technology (e.g., massspectrometry, infrared spectrometry, potentiostatic amperometry orUV/visible spectrophotometry). The tags detected can be correlated tothe particular DNA fragment under investigation as well as the identityof the mutant nucleotide.

10. Amplified Fragment Length Polymorphism (AFLP)

AFLP was designed as a highly sensitive method for DNA fingerprinting tobe used in a variety of fields, including plant and animal breeding,medical diagnostics, forensic analysis and microbial typing, to name afew. (Vos et al., Nucleic Acids Res. 23:4407-4414, 1995.) The power ofAFLP is based upon the molecular genetic variations that exist betweenclosely related species, varieties or cultivars. These variations in DNAsequence are exploited by the genetic fingerprinting technology suchthat “fingerprints” of particular genotypes can be routinely generated.These “fingerprints” are simply RFLPs visualized by selective PCRamplification of DNA restriction fragments. Briefly geneticfingerprinting technology consists of the following steps: genomic DNAis digested to completion by two different restriction enzymes. Specificdouble strand oligonucleotide adapters (˜25-30 bp) are ligated to therestricted DNA fragments. Oligonucleotide primers homologous to theadapters, but having extensions at the 3′-end are used to amplify asubset of the DNA fragments. (A pre-amplification step can also beperformed where the extension is only 1 bp in length. Amplification withthe primer having a 3 base-pair extension would follow.) Theseextensions can vary in length from 1 to 3 base-pair, but are of definedlength for a given primer. The sequence of the extension can also varyfrom one primer to another but is of a single, defined sequence within agiven primer. The selective nature of AFLP-PCR is based on the 3′extensions on the oligonucleotide primers. Since these extensions arenot homologous to adapter sequence, only DNA fragments complementary tothe extensions will be amplified due to the inability of Taq DNApolymerase, unlike some other DNA polymerases, to extend DNAs ifmismatches occur at the 3′-end of a molecule that is being synthesized.Therefore only a subset of the entire genome is amplified in anyreaction. For example, if 2 base-pair (bp) extensions are used, only onein 256 molecules is amplified. To further limit the number of fragmentsthat are actually visualized (so that a manageable number is observed),only one of the primers is labeled. Finally, the amplified DNAs areseparated on a polyacrylamide gel (sequencing type) and anautoradiograph or phosphor image is generated.

Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the technique of genetic fingerprinting. Briefly, such methodsgenerally comprise the steps of digesting (e.g., genomic DNA) tocompletion by two different restriction enzymes. Specific double-strandoligonucleotide adapters (˜25-30 bp) are ligated to the restricted DNAfragments. Optional pre-amplification utilizing primers with a 1 bpextension may be performed. The PCR product is then diluted, and taggedprimers homologous to the adapters, but having extensions at the 3′-endare used to amplify by PCR a subset of the DNA fragments. The resultingPCR products are then separated by size. The size separation step can beaccomplished by a variety of methods, including for example, HPLC. Thetags are then cleaved from the separated fragments, and detected by therespective detection technology (e.g., mass spectrometry, infraredspectrometry, potentiostatic amperometry or UV/visiblespectrophotometry).

11. Gene Expression Analysis

One of the inventions disclosed herein is a high throughput method formeasuring the expression of numerous genes (1-2000) in a singlemeasurement. The method also has the ability to be done in parallel withgreater than one hundred samples per process. The method is applicableto drug screening, developmental biology, molecular medicine studies andthe like. Within one aspect of the invention methods are provided foranalyzing the pattern of gene expression from a selected biologicalsample, comprising the steps of (a) exposing nucleic acids from abiological sample, (b) combining the exposed nucleic acids with one ormore selected tagged nucleic acid probes, under conditions and for atime sufficient for the probes to hybridize to the nucleic acids,wherein the tag is correlative with a particular nucleic acid probe anddetectable by non-fluorescent spectrometry, or potentiometry, (c)separating hybridized probes from unhybridized probes, (d) cleaving thetag from the tagged fragment, and (e) detecting the tag bynon-fluorescent spectrometry, or potentiometry, and therefromdetermining the pattern of gene expression of the biological sample.

Within a particularly preferred embodiment of the invention, assays ormethods are provided which are described as follows: RNA from a targetsource is bound to a solid support through a specific hybridization step(i.e., capture of poly(A) mRNA by a tethered oligo(dT) capture probe).The solid support is then washed and cDNA is synthesized on the solidsupport using standard methods (i.e., reverse transcriptase). The RNAstrand is then removed via hydrolysis. The result is the generation of aDNA population which is covalently immobilized to the solid supportwhich reflects the diversity, abundance, and complexity of the RNA fromwhich the cDNA was synthesized. The solid support then interrogated(hybridized) with 1 to several thousand probes that are complementary toa gene sequence of interest. Each probe type is labeled with a cleavablemass spectrometry tag or other type of cleavable tag. After theinterrogation step, excess or unhybridized probe is washed away, thesolid support is placed, for example, in the well of a microtiter plateand the mass spectrometry tag is cleaved from the solid support. Thesolid support is removed from the well of sample container, and thecontents of the well are measured with a mass spectrometer. Theappearance of specific mass spectrometer tags indicates the presence ofRNA in the sample and evidence that a specific gene is expressed in agiven biological sample. The method can also be quantifiable.

The compositions and methods for the rapid measurement of geneexpression using cleavable tags can be described in detail as follows.Briefly, tissue (liver, muscle, etc.), primary or transformed celllines, isolated or purified cell types or any other source of biologicalmaterial in which determining genetic expression is useful can be usedas a source of RNA. In the preferred method, the biological sourcematerial is lysed in the presence of a chaotrope in order to suppressnucleases and proteases and support stringent hybridization of targetnucleic acid to the solid support. Tissues, cells and biological sourcescan be effectively lysed in 1 to 6 molar chaotropic salts (guanidinehydrochloride, guanidine thiocyanate, sodium perchlorate, etc.). Afterthe source biological sample is lysed, the solution is mixed with asolid support to effect capture of target nucleic acid present in thelysate. In one permutation of the method, RNA is captured using atethered oligo(dT) capture probe. Solid supports can include nylonbeads, polystyrene microbeads, glass beads and glass surfaces or anyother type of solid support to which oligonucleotides can be covalentlyattached. The solid supports are preferentially coated with anamine-polymer such as polyethylene(imine), acrylamide,amine-dendrimers,. etc. The amines on the polymers are used tocovalently immobilize oligonucleotides. Oligonucleotides arepreferentially synthesized with a 5′-amine (generally a hexylamine thatincludes a six carbon spacer-arm and a distal amine). Oligonucleotidescan be 15 to 50 nucleotides in length. Oligonucleotides are activatedwith homo-bifunctional or hetero-bifunctional cross-linking reagentssuch as cyanuric chloride. The activated oligonucleotides are purifiedfrom excess cross-linking reagent (i.e., cyanuric chloride) by exclusionchromatography. The activated oligonucleotide are then mixed with thesolid supports to effect covalent attachment. After covalent attachmentof the oligonucleotides, the unreacted amines of the solid support arecapped (i.e., with succinic anhydride) to eliminate the positive chargeof the solid support. The solid supports can be used in parallel and arepreferentially configured in a 96-well or 384-well format. The solidsupports can be attached to pegs, stems, or rods in a 96-well or,384-well configuration, the solid supports either being detachable oralternatively integral to the particular configuration. The particularconfiguration of the solid supports is not of critical importance to thefunctioning of the assay, but rather, affects the ability of the assayto be adapted to automation. The solid supports are mixed with thelysate for 15 minutes to several hours to effect capture of the targetnucleic acid onto the solid support. In general, the “capture” of thetarget nucleic acid is through complementary base pairing of target RNAand the capture probe immobilized on the solid support. One permutationutilizes the 3′ poly(A) stretch found on most eucaryotic messengers RNAsto hybridize to a tethered oligo(dT) on the solid support. Anotherpermutation is to utilize a specific oligonucleotide or long probes(greater than 50 bases) to capture an RNA containing a defined sequence.Another possibility is to employ degenerate primers (oligonucleotides)that would effect the capture of numerous related sequences in thetarget RNA population. The sequence complexity of the RNA population andthe type of capture probe employed guide hybridization times.Hybridization temperatures are dictated by the type of chaotropeemployed and the final concentration of chaotrope (see Van Ness andChen, Nuc. Acids Res. 1991, for general guidelines). The lysate ispreferentially agitated continually with the solid support to effectdiffusion of the target RNA. Once the step of capturing the targetnucleic acid is accomplished, the lysate is washed from the solidsupport and all chaotrope or hybridization solution is removed. Thesolid support is preferentially washed with solutions containing ionicor non-ionic detergents, buffers and salts. The next step is thesynthesis of DNA complementary to the captured RNA. In this step, thetethered capture oligonucleotide serves as the extension primer forreverse transcriptase. The reaction is generally performed at 25 to 37°C. and preferably agitated during the polymerization reaction. After thecDNA is synthesized, it becomes covalently attached to the solid supportsince the capture oligonucleotide serves as the extension primer. TheRNA is then hydrolyzed from the cDNA/RNA duplex. The step can beeffected by the use of heat that denatures the duplex or the use of base(i.e., 0.1 N NaOH) to chemically hydrolyze the RNA. The key result atthis step is to make the cDNA available for subsequent hybridizationwith defined probes. The solid support or set of solid supports is thenfurther washed to remove RNA or RNA fragments. At this point, the solidsupport contains a approximate representative population of cDNAmolecules that represents the RNA population in terms of sequenceabundance, complexity, and diversity. The next step is to hybridizeselected probes to the solid support to identify the presence or absenceand the relative abundance of specific cDNA sequences. Probes arepreferentially oligonucleotides in length of 15 to 50 nucleotides. Thesequence of the probes is dictated by the end-user of the assay. Forexample, if the end-user intended to study gene expression in aninflammatory response in a tissue, probes would be selected to becomplementary to numerous cytokine mRNAs, RNAs that encode enzymes thatmodulate lipids, RNAs that encode factors that regulate cells involvedin an inflammatory response, etc. Once a set of defined sequences aredefined for study, each sequence is made into an oligonucleotide probeand each probe is assigned a specific cleavable tag. The tag(s) is thenattached to the respective oligonucleotide(s). The oligonucleotide(s)are hybridized to the cDNA on the solid support under appropriatehybridization conditions. After completion of the hybridization step;the solid support is washed to remove any unhybridized probe. The solidsupport or array of supports is then heated to cleave the covalent bondbetween the cDNA and the solid support. The tagged cDNA fragments arethen separated according to size by gel electrophoresis (e.g.,polyacrylamide gel electrophoresis) or preferably HPLC. The tags arethen cleaved from the DNA probe molecules, and detected by therespective detection technology (e.g., mass spectrometry, infraredspectrometry, potentiostatic amperometry or UV/visiblespectrophotometry). Each tag present is identified, and the presence(and abundance) or absence of an expressed mRNA is determined.

An alternative procedure would hybridize the tagged DNA probes directlyto the tethered mRNA target molecules under the appropriatehybridization conditions. After completion of the hybridization step,the solid support is washed to remove any unhybridized probe. The RNA isthen hydrolyzed from the DNA probe/RNA duplex. The step can be effectedby the use of heat which denatures the duplex or the use of base (i.e.,0.1 N NaOH) to chemically hydrolyze the RNA. This step will leave freemRNA and their corresponding DNA probes that can then be isolatedthrough a size separation step generally consisting of gelelectrophoresis (e.g., polyacrylamide gel electrophoresis) or preferablyHPLC. The tags are then cleaved from the DNA probe molecules, anddetected by the respective detection technology (e.g., massspectrometry, infrared spectrometry, potentiostatic amperometry orUV/visible spectrophotometry). Each tag present is identified, and thepresence (and abundance) or absence of an expressed mRNA is determined.

12. Hybridization Techniques

The successful cloning and sequencing of a gene leads to theinvestigation of its structure and expression by making it possible todetect the gene or its mRNA in a large pool of unrelated DNA or RNAmolecules. The amount of mRNA encoding a specific protein in a tissue isan important parameter for the activity of a gene and may besignificantly related to the activity of function systems. Itsregulation is dependent upon the interaction between sequences withinthe gene (cis-acting elements) and sequence-specific DNA bindingproteins (trans-acting factors), which are activated tissue-specificallyor by hormones and second messenger systems.

Several techniques are available for analysis of a particular gene, itsregulatory sequences, its specific mRNA and the regulation of itsexpression; these include Southern or Northern blot analysis andribonuclease (RNase) protection assay.

Variations in the nucleotide composition of a certain gene may be ofgreat pathophysiological relevance. When localized in the non-codingregions (5′, 3′-flanking regions and intron), they can affect theregulation of gene expression, causing abnormal activation orinhibition. When localized in the coding regions of the gene (exons),they may result in alteration of the protein function or dysfunctionalproteins. Thus, a certain sequence within a gene can correlate to aspecific disease and can be useful as a marker of the disease. Oneprimary goal of research in the medical field is, therefore, to detectthose genetic variations as diagnostic tools, and to gain importantinformation for the understanding of pathophysiological phenomena. Thebasic method for the analysis of a population regarding the variationswithin a certain gene is DNA analysis using the Southern blot technique.Briefly, prepared genomic DNA is digested with a restriction enzyme(RE), resulting in a large number of DNA fragments of different lengths,determined by the presence of the specific recognition site of the RE onthe genome. Alleles of a certain gene with mutations inside thisrestriction site will be cleaved into fragments of different number andlength. This is called restriction fragment length polymorphism (RFLP)and can be an important diagnostic marker with many applications. Thefragment to be analyzed has to be separated from the pool of DNAfragments and distinguished from other DNA species using a specificprobe. Thus, DNA is subjected to electrophoretic fractionation using anagarose gel, followed by transfer and fixation to a nylon ornitrocellulose membrane. The fixed, single-stranded DNA is hybridized toa tagged DNA that is complementary to the DNA to be detected, Afterremoving non-specific hybridizations, the DNA fragment of interest canbe visualized according to the probes characteristics (autoradiographyor phosphor image analysis).

Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the techniques similar to Southern blotting. Briefly, suchmethods generally comprise the steps of generating a series of taggednucleic acid fragments in which the fragments generated are digestedwith restriction enzymes. The tagged fragments are generated byconducting a hybridization step of the tagged probes with the digestedtarget nucleic acid. The hybridization step can take place prior to orafter the restriction nuclease digestion. The resulting digested nucleicacid fragments are then separated by size. The size separation step canbe accomplished, for example, by gel electrophoresis (e.g.polyacrylamide gel electrophoresis) or preferably HPLC. The tags arethen cleaved from the separated fragments, and then the tags aredetected by the respective detection technology (e.g., massspectrometry, infrared spectrometry, potentiostatic amperometry orUV/visible spectrophotometry).

The presence and quantification of a specific gene transcript and itsregulation by physiological parameters can be analyzed by means ofNorthern blot analysis and RNase protection assay. The principle basisof these methods is hybridization of a pool of total cellular RNA to aspecific probe. In the Northern blot technique, total RNA of a tissue isfractionated using an HPLC or LC method, hybridized to a labeledantisense RNA (cRNA), complementary to the RNA to be detected. Byapplying stringent washing conditions, non-specifically bound moleculesare eliminated. Specifically bound molecules, would subsequently bedetected according to the type of probe utilized (mass spectrometry, orwith a electrochemical detector). In addition, specificity can becontrolled by comparing the size of the detected mRNA with the predictedlength of the mRNA of interest.

Within one embodiment of the invention methods are provided fordetermining the identity of a ribonucleic acid molecule, or fordetecting a selecting ribonucleic acid molecule, in, for example abiological sample, utilizing the techniques similar to Northernblotting. Briefly, such methods generally comprise the steps ofgenerating a series of tagged RNA molecules by conducting ahybridization step of the tagged probes with the target RNA. The taggedRNA molecules are then separated by size. The size separation step canbe accomplished, for example by preferably HPLC. The tags are cleavedfrom the separated RNA molecules, and then the tags are detected by therespective detection technology (e.g., mass spectrometry, infraredspectrometry, potentiostatic amperometry or UV/visiblespectrophotometry).

The most specific method for detection of a mRNA species is the RNaseprotection assay. Briefly, total RNA from a tissue or cell culture ishybridized to a tagged specific cRNA of complete homology. Specificityis accomplished by subsequent RNase digestion. Non-hybridized,single-stranded RNA and non-specifically hybridized fragments with evensmall mismatches will be recognized and cleaved, while double-strandedRNA of complete homology is not accessible to the enzyme and will beprotected. After removing RNase by proteinase K digestion and phenolextraction, the specific protected fragment can be separated fromdegradation products, usually by HPLC.

Within one embodiment of the invention methods are provided fordetermining the identity of a ribonucleic acid molecule, or fordetecting a selecting ribonucleic acid molecule, in, for example abiological sample, utilizing the technique of RNase protection assay.Briefly, such methods generally comprise the steps of total RNA from atissue or cell culture being hybridized to a tagged specific cRNA ofcomplete homology, a RNase digestion, treatment with proteinase K and aphenol extraction. The tagged, protected RNA fragment is isolated fromthe degradation products. The size separation step can be accomplished,for example by LC or HPLC. The tag is cleaved from the separated RNAmolecules, and then is detected by the respective detection technology(e.g., mass spectrometry, infrared spectrometry, potentiostaticamperometry or UV/visible spectrophotometry).

13. Mutation Detection Techniques

The detection of diseases is increasingly important in prevention andtreatments. While multifactorial diseases are difficult to devisegenetic tests for, more than 200 known human disorders are caused by adefect in a single gene, often a change of a single amino acid residue(Olsen, Biotechnology: An industry comes of age, National AcademicPress, 1986). Many of these mutations result in an altered amino acidthat causes a disease state.

Sensitive mutation detection techniques offer extraordinarypossibilities for mutation screening. For example, analyses may beperformed even before the implantation of a fertilized egg (Holding andMonk, Lancet 3:532, 1989). Increasingly efficient genetic tests may alsoenable screening for oncogenic mutations in cells exfoliated from therespiratory tract or the bladder in connection with health checkups(Sidransky et al., Science 252:706, 1991). Also, when an unknown genecauses a genetic disease, methods to monitor DNA sequence variants areuseful to study the inheritance of disease through genetic linkageanalysis. However, detecting and diagnosing mutations in individualgenes poses technological and economic challenges. Several differentapproaches have been pursued, but none are both efficient andinexpensive enough for truly wide-scale application.

Mutations involving a single nucleotide can be identified in a sample byphysical, chemical, or enzymatic means. Generally, methods for mutationdetection may be divided into scanning techniques, which are suitable toidentify previously unknown mutations, and techniques designed todetect, distinguish, or quantitate known sequence variants. Severalscanning techniques for mutation detection have been developed inheteroduplexes of mismatched complementary DNA strands, derived fromwild type and mutant sequences, exhibit an abnormal behavior especiallywhen denatured. This phenomenon is exploited in denaturing andtemperature gradient gel electrophoresis (DGGE and TGGE, respectively)methods. Duplexes mismatched in even a single nucleotide position canpartially denature, resulting in retarded migration, whenelectrophoresed in an increasingly denaturing gradient gel (Myers etal., Nature 313:495, 1985; Abrades et al., Genomics 7:463, 1990; Hencoet al., Nucl. Acids Res. 18:6733, 1990). Although mutations may bedetected, no information is obtained regarding the precise location of amutation. Mutant forms must be further isolated and subjected to DNAsequence analysis. Alternatively, RNase A may cleave a heteroduplex ofan RNA probe and a target strand at a position where the two strands arenot properly paired. The site of cleavage can then be determined byelectrophoresis of the denatured probe. However, some mutations mayescape detection because not all mismatches are efficiently cleaved byRNase A. Mismatched bases in a duplex are also susceptible to chemicalmodification. Such modifications can render the strands susceptible tocleavage at the site of the mismatch or cause a polymerase to stop in asubsequent extension reaction. The chemical cleavage technique allowsidentification of a mutation in target sequences of up to 2 kb and itprovides information on the approximate location of mismatchednucleotide(s) (Cotton et al., PNAS USA 85:4397, 1988; Ganguly et al.,Nucl. Acids Res. 18:3933, 1991). However, this technique is laborintensive and may not identify the precise location of the mutation.

An alternative strategy for detecting a mutation in a DNA strand is bysubstituting (during synthesis) one of the normal nucleotides with amodified nucleotide, altering the molecular weight or other physicalparameter of the product. A strand with an increased or decreased numberof this modified nucleotide relative to the wild-type sequence exhibitsaltered electrophoretic mobility (Naylor et al., Lancet 337:635, 1991).This technique detects the presence of a mutation, but does not providethe location.

Two other strategies visualize mutations in a DNA segment by altered gelmigration. In the single-strand conformation polymorphism technique(SSCP), mutations cause denatured strands to adopt different secondarystructures, thereby influencing mobility during native gelelectrophoresis. Heteroduplex DNA molecules, containing internalmismatches, can also be separated from correctly matched molecules byelectrophoresis (Orita, Genomics 5:874, 1989; Keen, Trends Genet. 7:5,1991). As with the techniques discussed above, the presence of amutation may be determined but not the location. As well, many of thesetechniques do not distinguish between a single and multiple mutations.All of the above-mentioned techniques indicate the presence of amutation in a limited segment of DNA and some of them allow approximatelocalization within the segment. However, sequence analysis is stillrequired to unravel the effect of the mutation on the coding potentialof the segment. Sequence analysis is very powerful, allowing, forexample, screening for the same mutation in other individuals of anaffected family, monitoring disease progression in the case of malignantdisease or for detecting residual malignant cells in the bone marrowbefore autologous transplantation. Despite these advantages, theprocedure is unlikely to be adopted as a routine diagnostic methodbecause of the high expense involved.

A large number of other techniques have been developed to analyze knownsequence variants. Automation and economy are very importantconsiderations for these types of analyses that may be applied, forscreening individuals and the general population. None of the techniquesdiscussed below combine economy and automation with the requiredspecificity.

Mutations may be identified via their destabilizing effects on thehybridization of short oligonucleotide probes to a target sequence (seeWetmur, Crit. Rev. Biochem. Mol. Biol. 26:227, 1991). Generally, thistechnique, allele-specific oligonucleotide hybridization, involvesamplification of target sequences and subsequent hybridization withshort oligonucleotide probes. An amplified product can thus be scannedfor many possible sequence variants by determining its hybridizationpattern to an array of immobilized oligonucleotide probes. However,establishing conditions that distinguish a number of other strategiesfor nucleotide sequence distinction all depend on enzymes to identifysequence differences (Saiki, PNAS USA 86:6230, 1989; Zhang, Nucl. AcidsRes. 19:3929, 1991).

For example, restriction enzymes recognize sequences of about 4-8nucleotides. Based on an average G+C content, approximately half of thenucleotide positions in a DNA segment can be monitored with a panel of100 restriction enzymes. As an alternative, artificial restrictionenzyme recognition sequences may be created around a variable positionby using partially mismatched PCR primers. With this technique, eitherthe mutant or the wild-type sequence alone may be recognized and cleavedby a restriction enzyme after amplification (Chen et al., Anal. Biochem.195:51, 1991; Levi et al., Cancer Res. 51:3497, 1991). Another methodexploits the property that an oligonucleotide primer that is mismatchedto a target sequence at the 3′ penultimate position exhibits a reducedcapacity to serve as a primer in PCR. However, some 3′ mismatches,notably G−T, are less inhibitory than others limiting its usefulnessare. In attempts to improve this technique, additional mismatches areincorporated into the primer at the third position from the 3′ end. Thisresults in two mismatched positions in the three 3′ nucleotides of theprimer hybridizing with one allelic variant, and one mismatch in thethird position in from the 3′ end when the primer hybridizes to theother allelic variant (Newton et al., Nucl. Acids Res. 17:2503, 1989).It is necessary to define amplification conditions that significantlyfavor amplification of a 1 bp mismatch.

DNA polymerases have also been used to distinguish allelic sequencevariants by determining which nucleotide is added to an oligonucleotideprimer immediately upstream of a variable position in the target strand.

A ligation assay has been developed. In this method, two oligonucleotideprobes hybridizing in immediate juxtaposition on a target strand arejoined by a DNA ligase. Ligation is inhibited if there is a mismatchwhere the two oligonucleotide probes abut.

14. Assays for Mutation Detection

Mutations are a single-base pair change in genomic DNA. Within thecontext of this invention, most such changes are readily detected byhybridization with oligonucleotides that are complementary to thesequence in question. In the system described here, two oligonucleotidesare employed to detect a mutation. One oligonucleotide possesses thewild-type sequence and the other oligonucleotide possesses the mutantsequence. When the two oligonucleotides are used as probes on awild-type target genomic sequence, the wild-type oligonucleotide willform a perfectly based paired structure and the mutant oligonucleotidesequence will form a duplex with a single base pair mismatch. Asdiscussed above, a 6 to 7° C. difference in the Tm of a wild type versusmismatched duplex permits the ready identification or discrimination ofthe two types of duplexes. To effect this discrimination, hybridizationis performed at the Tm of the mismatched duplex in the respectivehybotropic solution. The extent of hybridization is then measured forthe set of oligonucleotide probes. When the ratio of the extent ofhybridization of the wild-type probe to the mismatched probe ismeasured, a value to 10/1 to greater than 20/1 is obtained. These typesof results permit the development of robust assays for mutationdetection.

For exemplary purposes, one assay format for mutation detection utilizestarget nucleic acid (e.g., genomic DNA) and oligonucleotide probes thatspan the area of interest. The oligonucleotide probes are greater orequal to 24 nt in length (with a maximum of about 36 nt) and labeledwith a fluorochrome at the 3′ or 5′ end of the oligonucleotide probe.The target nucleic acid is obtained via the lysis of tissue culturecells, tissues, organisms, etc., in the respective hybridizationsolution. The lysed solution is then heated to a temperature thatdenatures the target nucleic acid (15-25° C. above the Tm of the targetnucleic acid duplex). The oligonucleotide probes are added at thedenaturation temperature, and hybridization is conducted at the Tm ofthe mismatched duplex for 0.5 to 24 hours. The genomic DNA is thencollected and by passage through a GF/C (GF/B, and the like) glass fiberfilter. The filter is then washed with the respective hybridizationsolution to remove any non-hybridized oligonucleotide probes (RNA, shortoligos and nucleic acid does not bind to glass fiber filters under theseconditions). The hybridization oligo probe can then be thermally elutedfrom the target DNA and measured (by fluorescence for example). Forassays requiring very high levels of sensitivity, the probes areconcentrated and measured.

Other highly sensitive hybridization protocols may be used. The methodsof the present invention enable one to readily assay for a nucleic acidcontaining a mutation suspected of being present in cells, samples,etc., i.e., a target nucleic acid. The target nucleic acid contains thenucleotide sequence of deoxyribonucleic acid (DNA) or ribonucleic acid(RNA) whose presence is of interest, and whose presence or absence is tobe detected for in the hybridization assay. The hybridization methods ofthe present invention may also be applied to a complex biologicalmixture of nucleic acid (RNA and/or DNA). Such a complex biologicalmixture includes a wide range of eucaryotic and procaryotic cells,including protoplasts; and/or other biological materials which harborpolynucleotide nucleic acid. The method is thus applicable to tissueculture cells, animal cells, animal tissue, blood cells (e.g.,reticulocytes, lymphocytes), plant cells, bacteria, yeasts, viruses,mycoplasmas, protozoa, fungi and the like. By detecting a specifichybridization between nucleic acid probes of a known source, thespecific presence of a target nucleic acid can be established. A typicalhybridization assay protocol for detecting a target nucleic acid in acomplex population of nucleic acids is described as follows: Targetnucleic acids are separated by size on an LC or HPLC, cloned andisolated, sub-divided into pools, or left as a complex population.Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the general techniques of hybridization assays. Briefly, suchmethods generally comprise the steps of target nucleic acids beingcloned and isolated, sub-divided into pools, or left as a complexpopulation. The target nucleic acids are hybridized with taggedoligonucleotide probes under conditions described above. The targetnucleic acids are separated according to size by LC or HPLC. The tagsare cleaved from the separated fragments, and then the tags are detectedby the respective detection technology (e.g., mass spectrometry,infrared spectrometry, potentiostatic amperometry or UV/visiblespectrophotometry).

15. Sequencing by Hybridization

DNA sequence analysis is conventionally performed by hybridizing aprimer to target DNA and performing chain extensions using a polymerase.Specific stops are controlled by the inclusion of a dideoxynucleotide.The specificity of priming in this type of analysis can be increased byincluding a hybotrope in the annealing buffer and/or incorporating anabasic residue in the primer and annealing at a discriminatingtemperature.

Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the general techniques of sequencing by hybridization usingthe Sanger method. Briefly, such methods generally comprise the steps ofhybridizing a tagged primer to target DNA and performing chainextensions using a polymerase. Specific stops are controlled by theinclusion of a dideoxynucleotide that may also be tagged. The targetnucleic acids are separated according to size by HPLC. The tags arecleaved from the separated fragments, and are detected by the respectivedetection technology (e.g., mass spectrometry, infrared spectrometry,potentiostatic amperometry or UV/visible spectrophotometry). Othersequence analysis methods involve hybridization of the target with anassortment of random, short oligonucleotides. The sequence isconstructed by overlap hybridization analysis. In this technique,precise hybridization is essential. Use of hybotropes or abasic residuesand annealing at a discriminating temperature is beneficial for thistechnique to reduce or eliminate mismatched hybridization. The goal isto develop automated hybridization methods in order to probe largearrays of oligonucleotide probes or large arrays of nucleic acidsamples. Applications of such technologies include gene mapping, clonecharacterization, medical genetics and gene discovery, DNA sequenceanalysis by hybridization, and finally, sequencing verification. Manyparameters must be controlled in order to automate or multiplexoligonucleotide probes. The stability of the respective probes must besimilar, the degree of mismatch with the target nucleic acid, thetemperature, ionic strength, the A+T content of the probe (or target),as well as other parameters when the probe is short (i.e., 6 to 50nucleotides) should be similar. Usually, the conditions of theexperiment and the sequence of the probe are adjusted until theformation of the perfectly based-paired probe is thermodynamicallyfavored over the any duplex that contains a mismatch. Very large-scaleapplications of probes such as sequencing by hybridization (SBH), ortesting highly polymorphic loci such as the cystic fibrosistrans-membrane protein locus require a more stringent level of controlof multiplexed probes. Within one embodiment of the invention methodsare provided for determining the identity of a nucleic acid molecule, orfor detecting a selecting nucleic acid molecule, in, for example abiological sample, utilizing the general techniques of sequencing byhybridization. Briefly, such methods generally comprise of hybridizing aseries of tagged primers to a DNA target or a series of target DNAfragments under carefully controlled conditions. The target nucleicacids are separated according to size by HPLC. The tags are then cleavedfrom the separated fragments, and detected by the respective detectiontechnology (e.g., mass spectrometry, infrared spectrometry,potentiostatic amperometry or UV/visible spectrophotometry).

16. Oligonucleotide-ligation Assay

Oligonucleotide-ligation assay is an extension of PCR-based screeningthat uses an ELISA-based assay (OLA, Nickerson et al., Proc. Natl. Acad.Sci. USA 15 87:8923, 1990) to detect the PCR products that contain thetarget sequence. Thus, both gel electrophoresis and colony hybridizationare eliminated. Briefly, the OLA employs two adjacent oligonucleotides:a “reporter” probe (tagged at the 5′ end) and a5′-phosphorylated/3′-biotinylated “anchor” probe. The twooligonucleotides, which are complementary to sequences internal to thePCR primers, are annealed to target DNA and, if there is perfectcomplementarity, the two probes are ligated by T4 DNA ligase. Capture ofthe biotinylated anchor probe on immobilized streptavidin and analysisfor the covalently linked reporter probe test for the presence orabsence of the target sequences among the PCR products. Within oneembodiment of the invention methods are provided for determining theidentity of a nucleic acid molecule, or for detecting a selectingnucleic acid molecule, in, for example a biological sample, utilizingthe technique of oligonucleotide ligation assay. Briefly, such methodsgenerally comprise the steps of performing PCR on the target DNAfollowed by hybridization with the 5′ tagged ireporteri DNA probe and a5′ phosphorylated/non-biotinylated probe. The sample is incubated withT4 DNA ligase. The DNA strands with ligated probes can be separated fromthe DNA with non-ligated probes by, for example, preferably by LC orHPLC. The tags are cleaved from the separated fragments, and then thetags are detected by the respective detection technology (e.g., massspectrometry, infrared spectrophotometry, potentiostatic amperometry orUV/visible spectrophotometry. Recent advances in the OLA assay haveallowed for the analysis multiple samples and multiple mutationsconcurrently. (Baron et al., Nature Biotechnology 87:1279, 1996.)Briefly, the method consists of amplifying the gene fragment containingthe mutation of interest with PCR. The PCR product is then hybridizedwith a common and two allele-specific oligonucleotide probes (onecontaining the mutation while the other does not) such that the 3′ endsof the allele-specific probes are immediately adjacent to the 5′ end ofthe common probe. This sets up a competitive hybridization-ligationprocess between the two allelic probes and the common probe at eachlocus. The thermostable DNA ligase then discriminates betweensingle-base mismatches at the junction site, thereby producingallele-specific ligation products. The common probe is labeled with oneof four fluorophores and the allele-specific probes are each labeledwith one or more pentaethyleneoxide mobility modifying tails whichprovide a sizing difference between the different allele-specificprobes. The samples are then separated by gel electrophoresis based uponthe length of the modifying tails and detected by the fluorescent tag onthe common probe. Through the use in sizing differences on theallele-specific probes and four fluorophores available for the commonprobe, many samples can be analyzed on one lane of the electrophoreticgel. Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the technique of oligonucleotide ligation assay for concurrentmultiple sample detection. Briefly, such methods generally comprise thesteps of performing PCR on the target DNA followed by hybridization withthe common probe (untagged) and two allele-specific probes taggedaccording to the specifications of the invention. The sample isincubated with DNA ligase and fragments separated by, for example,preferably by LC or HPLC. The tags are cleaved from the separatedfragments, and then the tags are detected by the respective detectiontechnology (e.g., mass spectrometry, infrared spectrophotometry,potentiostatic amperometry or UV/visible spectrophotometry.

17. Differential Display

a. Overview

Mammals, such as human beings, have about 100,000 different genes intheir genome, of which only a small fraction, perhaps 15%, are expressedin any individual cell. The choice of genes expressed determine thebiochemical character of any given cell or tissue. The process of normalcellular growth and differentiation, as well as the pathological changesthat arise in diseases like cancer, are all driven by changes in geneexpression. Differential display methods permits the identification ofgenes specifically expressed in individual cell types.

The differential display technique amplifies the 3′ terminal portions ofcorresponding cDNAs by using a primer designed to bind to the 5′boundary of a poly(A) tail and primers of, arbitrary sequence that bindupstream. Amplified populations with each primer pair are visualized bya size separation method (PAGE, HPLC, etc.), allowing direct comparisonof the mRNAs between two biological samples of interest. Thedifferential display method has the potential to visualize all theexpressed genes (about 10,000 to 15,000 mRNA species) in a mammaliancell and enables sequence analysis. It is possible to compare: (1) thetotal number of peaks amplified in the parents, (2) the number ofpolymorphic peaks between parents, and (3) the segregation ratios ofpolymorphic peaks in the progeny of crosses in animals or plants.Differential display is also used for the identification of up- anddown-regulated genes, known or unknown, after a variety of stimuli.Differential display PCR fragments can be used as probes for cDNAcloning (discovering an unknown gene from a cDNA or genomic library).

Briefly, the steps in differential display are as follows: 1) RNA isisolated from biological sample of interest. Total RNA, cytoplasmic RNAor mRNA can be used. 2) first strand cDNAs are generated using ananchored oligodT(oligodTdN, where N is A, C, or G). 3) Amplification ofcDNA using oligodTdN and short primers with arbitrary sequence. For acomplete differential display analysis of two cell populations or twosamples of interest, 9 different primers are required. The detectionlimit of differential display for a specific mRNA is less than 0.001% ofthe total mRNA population.

Because of the simplicity, sensitivity, and reproducibility of themethod disclosed here, the CMST differential display method is asignificant advance over traditional gel based systems. With theCMST-based differential display analysis of two cell types, including64×24 PCR runs can be completed rapidly as opposed to a labor intensive,lengthy time by the traditional method. Moreover, sequence heterogeneityof bands isolated from differential display gels has been found to be acontributing factor to the high failure rate of this technique. This iscompletely avoided with the CMST-based differential display methologydescribed here.

b. CMST-based Differential Display Example.

The starting material for differential display is RNA isolated from twodifferent populations of cells. Generally, the cells are of similarorigin, and differ with respect to their treatment with drugs, theirbeing “normal” versus “transformed”, or their expression of variousintroduced genes.

Plant tissue or animal material (2-3 g) is harvested and minced orchopped in sterile petri dishes. The material is then ground to a finepowder in a precooled pestle and mortar under liquid N₂. 1 g of frozenpowder is transferred to a 12 ml poly-propelene tubes (1 g ca. 5 mlpowder) containing 8 ml of a hot (80° C.) 1:1 mixture of RNA extractionbuffer (100 mM Tris-HCl (pH 8.0), 100 mM LiCl, 10 mM EDTA, 1.0% LiDS)and phenol (base vol.: 4 ml). The sample is mixed (vortexed) at highspeed for at least 30 seconds. A volume of chloroform is added (4 ml)and again mixed and spun for 20 mins in a centrifuge at 5000 to10,000×g. The aqueous phase is transferred to a new 12 ml tube and 1/3volume of cold 8M LiCl is added to precipitate the RNA (3 h at 0° C.).The RNA is centrifuged at 0° C. for 20 mins and resuspended in 1 ml H₂O.Residual genomic DNA is removed by treating the RNA sample with DNase I.Reverse transcription is performed on each RNA sample using 500 ng ofDNA free RNA in 1× reverse transcription buffer, 10 mM DTT, 20 μM dNTPs,0.2 μM 5′RS H-T11C (one base anchored primer with 5′ restriction site),200 U MoMuLV reverse transcriptase and 1.5U RNA Guard per 20 μl reactionvolume.

Although using a downstream primer reduces the number of cDNAsubfractions to three, it does not reduce the number of PCR reactionsrequired to display most of the cDNA species present in the pool. On thecontrary, it decreases the theoretical chance of identifying those cDNAspecies which are present. The best results are obtained using acombination of nine different primers of the type DMO-VV, where V can beA,G,C but not T. With a T in the terminal 3′ position, incompletehybridization of the primer leads to smearing of bands on the gels. Theoptimal concentration of RNA is 200-300 ng per cDNA synthesis.

CMST-based differential display is performed essentially as previouslydescribed (Liang and Pardee, Science 257:967-971, 1992) except for thedesign of primers used for reverse transcription and amplificationsteps, and the choice of radiolabeled nucleotide. A completedifferential display analysis of the cDNAs from two biological samplesof interest using nine downstream primers and 24 upstream primers wouldgenerate 9×24×2 CMST-based differential display reactions Amplificationproducts can be separated by HPLC and reamplified if desired.

Following incubation of the RNA at 65° C. for 5 minutes, samples arechilled on ice, added to the reverse transcription mix and incubated for60 minutes at 37° C. followed by 95° C. for 5 minutes. Duplicate cDNAsamples are then amplified using the same 5′-primer in combination witha series of 13 mers of arbitrary but defined sequence: H-AP:AAGCTTCGACTGT (Seq. ID No. 2), H-AP: AAGCTTTGGTCAG (Seq. ID No. 3),H-AP4: AAGCTTCTCAACG (Seq. ID No. 4), H-AP5: AAGCTTAGTAGGC (Seq. ID No.5).

Amplification is performed in reaction mixes containing 0.1× volume ofreverse transcription reaction, 1×PCR buffer (10×PCR buffer=100 mMTRIS-HCl, 15 mM MgCl2, 10 mM KCl pH 8.3) 2 μM dNTPs, 0.2 μM RS H-T11Canchored primer, 0.2 μM appropriate arbitrary primer, 1.5 U Expand™ highfidelity DNA polymerase, and water to a final volume of 20 μl.Amplification of the cDNA is performed under the following conditions:94° C. (1 minute) followed by 40 cycles of 94° C. (30 seconds), 40° C.(2 minutes), 72° C. (30 seconds) and finished with 72° C. (5 minutes).

Amplification for each gene is performed with gene specific primersspanning a known intron/exon boundry (see tables below). Allamplifications are done in 20 μl volumes containing 10 mM Tris HCl pH8.3, 1 mM NH4Cl, 1.5 M MgCl2, 100 mM KCl, 0.125 mM NTPs, 10 ng/ml of therespective oligonucleotide primers and 0.75 units of Taq DNA polymerase(Gibco-BRL). Cycling parameters were 94° C. preheating step for 5minutes followed by 94° C. denaturing step for 1 minute, 55° C.annealing step for 2 minutes, and a 72° C. extension step for 30 secondsto 1 minute and a final extension at 72° C. for 10 minutes.Amplification cycles are generally 30-45 in number.

Amplification products are gel purified (Zhen and Swank, BioTechniques14::894-898, 1993) on 1% agarose gels run in 0.04 M Tris-acetate, 0.001M EDTA (1×TEA) buffer and stained with ethidium bromide. A trough is cutjust in front of the band of interest and filled with 50-200 μl of 10%PEG in 1×TAE buffer. Electrophoresis is continued until the band hascompletely entered the trough. The contents are then removed andextracted with phenol, cholorform extracted, and precipitated in 0.1volume of 7.5 M ammonium acetate and 2.5 volumes of 100% EtOH. Samplesare washed with 75% EtOH and briefly dried at ambient temperature.Quantitation of yield is done by electrophoresis of a small aliquot on1% agarose gel in 1×TBE buffer with ethidium bromide staining andcomparison to a known standard.

The products from the amplification reactions are analyzed by HPLC. HPLCias carried out using automated HPLC instrumentation (Rainin,Emeryville, Calif., or Hewlett Packard, Palo Alto, Calif.). UnpurifiedDNA fingerprinting products which are denatured for 3 minutes at 95prior into injection into an HPLC are eluted with linear acetonitrile(ACN, J. T. Baker, N.J.) gradient of 1.8%/minute at a flow rate of 0.9ml/minute. The start and end points are adjusted according to the sizeof the amplified products. The temperature required for the successfulresolution of the molecules generated during the DNA fingerprintingtechnique is 50° C. The effluent from the HPLC is then directed into amass spectrometer (Hewlett Packard, Palo Alto, Calif.) for the detectionof tags.

Comparison of the chromatograms (mass spectrometry-based) indicates thatbands at 220 bp and 468 bp are observed in the stimulated Jurkat cellsand not observed in the unstimulated Jurkat cells.

C. Separation of Nucleic Acid Fragments

A sample that requires analysis is often a mixture of many components ina complex matrix. For samples containing unknown compounds, thecomponents must be separated from each other so that each individualcomponent can be identified by other analytical methods. The separationproperties of the components in a mixture are constant under constantconditions, and therefore once determined they can be used to identifyand quantify each of the components. Such procedures are typical inchromatographic and electrophoretic analytical separations.

1. High-Performance Liquid Chromatography (HPLC)

High-Performance liquid chromatography (HPLC) is a chromatographicseparations technique to separate compounds that are dissolved insolution. HPLC instruments consist of a reservoir of mobile phase, apump, an injector, a separation column, and a detector. Compounds areseparated by injecting an aliquot of the sample mixture onto the column.The different components in the mixture pass through the column atdifferent rates due to differences in their partitioning behaviorbetween the mobile liquid phase and the stationary phase.

Recently, IP-RO-HPLC on non-porous PS/DVB particles with chemicallybonded alkyl chains have been shown to be rapid alternatives tocapillary electrophoresis in the analysis of both single anddouble-strand nucleic acids providing similair degrees of resolution(Huber et al, Anal.Biochem. 212:351, 1993; Huber et al., 1993, Nuc.Acids Res. 21:1061; Huber et al., Biotechniques 16:898, 1993). Incontrast to ion-excahnge chromoatrography, which does not always retaindouble-strand DNA as a function of strand length (Since AT base pairsintereact with the positively charged stationary phase, more stronglythan GC base-pairs), IP-RP-HPLC enables a strictly size-dependentseparation.

A method has been developed using 100 mM triethylammonium acetate asion-pairing reagent, phosphodiester oligonucleotides could besuccessfully separated on alkylated non-porous 2.3 μMpoly(styrene-divinylbenzene) particles by means of high performanceliquid chromatography (Oefner et al., Anal. Biochem. 223:39, 1994). Thetechnique described allowed the separation of PCR products differingonly 4 to 8 base pairs in length within a size range of 50 to 200nucleotides.

2. Electrophoresis

Electrophoresis is a separations technique that is based on the mobilityof ions (or DNA as is the case described herein) in an electric field.Negatively charged DNA charged migrate towards a positive electrode andpositively-charged ions migrate toward a negative electrode. For safetyreasons one electrode is usually at ground and the other is biasedpositively or negatively. Charged species have different migration ratesdepending on their total charge, size, and shape, and can therefore beseparated. An electrode apparatus consists of a high-voltage powersupply, electrodes, buffer, and a support for the buffer such as apolyacrylamide gel, or a capillary tube. Open capillary tubes are usedfor many types of samples and the other gel supports are usually usedfor biological samples such as protein mixtures or DNA fragments.

3. Capillary Electrophoresis (CE)

Capillary electrophoresis (CE) in its various manifestations (freesolution, isotachophoresis, isoelectric focusing, polyacrylamide gel,micellar electrokinetic “chromatography”) is developing as a method forrapid high resolution separations of very small sample volumes ofcomplex mixtures. In combination with the inherent sensitivity andselectivity of MS, CE-MS is a potential powerful technique forbioanalysis. In the novel application disclosed herein, the interfacingof these two methods will lead to superior DNA sequencing methods thateclipse the current rate methods of sequencing by several orders ofmagnitude.

The correspondence between CE and electrospray ionization (ESI) flowrates and the fact that both are facilitated by (and primarily used for)ionic species in solution provide the basis for an extremely attractivecombination. The combination of both capillary zone electrophoresis(CZE) and capillary isotachophoresis with quadrapole mass spectrometersbased upon ESI have been described (Olivares et al., Anal. Chem.59:1230, 1987; Smith et al., Anal. Chem. 60:436, 1988; Loo et al., Anal.Chem. 179:404, 1989; Edmonds et al., J. Chroma. 474:21, 1989; Loo etal., J. Microcolumn Sep. 1:223, 1989; Lee et al., J. Chromatog. 458:313,1988; Smith et al., J. Chromatog. 480:211, 1989; Grese et al., J. Am.Chem. Soc. 111:2835, 1989). Small peptides are easily amenable to CZEanalysis with good (femtomole) sensitivity.

The most powerful separation method for DNA fragments is polyacrylamidegel electrophoresis (PAGE), generally in a slab gel format. However, themajor limitation of the current technology is the relatively long timerequired to perform the gel electrophoresis of DNA fragments produced inthe sequencing reactions. An increase magnitude (10-fold) can beachieved with the use of capillary electrophoresis which utilizeultrathin gels. In free solution to a first approximation all DNAmigrate with the same mobility as the addition of a base results in thecompensation of mass and charge. In polyacrylamide gels, DNA fragmentssieve and migrate as a function of length and this approach has now beenapplied to CE. Remarkable plate number per meter has now been achievedwith cross-linked polyacrylamide (10⁻⁷ plates per meter, Cohen et al.,Proc. Natl. Acad. Sci., USA 85:9660, 1988). Such CE columns as describedcan be employed for DNA sequencing. The method of CE is in principle 25times faster than slab gel electrophoresis in a standard sequencer. Forexample, about 300 bases can be read per hour. The separation speed islimited in slab gel electrophoresis by the magnitude of the electricfield which can be applied to the gel without excessive heat production.Therefore, the greater speed of CE is achieved through the use of higherfield strengths (300 V/cm in CE versus 10 V/cm in slab gelelectrophoresis). The capillary format reduces the amperage and thuspower and the resultant heat generation.

Smith and others (Smith et al., Nuc. Acids. Res. 18:4417, 1990) havesuggested employing multiple capillaries in parallel to increasethroughput. Likewise, Mathies and Huang (Mathies and Huang, Nature359:167, 1992) have introduced capillary electrophoresis in whichseparations are performed on a parallel array of capillaries anddemonstrated high through-put sequencing (Huang et al., Anal. Chem.64:967, 1992, Huang et al., Anal. Chem. 64:2149, 1992). The majordisadvantage of capillary electrophoresis is the limited amount ofsample that can be loaded onto the capillary. By concentrating a largeamount of sample at the beginning of the capillary, prior to separation,loadability is increased, and detection levels can be lowered severalorders of magnitude. The most popular method of preconcentration in CEis sample stacking. Sample stacking has recently been reviewed (Chienand Burgi, Anal. Chem. 64:489A, 1992). Sample stacking depends of thematrix difference, (pH, ionic strength) between the sample buffer andthe capillary buffer, so that the electric field across the sample zoneis more than in the capillary region. In sample stacking, a large volumeof sample in a low concentration buffer is introduced forpreconcentration at the head of the capillary column. The capillary isfilled with a buffer of the same composition, but at higherconcentration. When the sample ions reach the capillary buffer and thelower electric field, they stack into a concentrated zone. Samplestacking has increased detectabilities 1-3 orders of magnitude.

Another method of preconcentration is to apply isotachophoresis (ITP)prior to the free zone CE separation of analytes. ITP is anelectrophoretic technique which allows microliter volumes of sample tobe loaded on to the capillary. in contrast to the low nL injectionvolumes typically associated with CE. The technique relies on insertingthe sample between two buffers (leading and trailing electrolytes) ofhigher and lower mobility respectively, than the analyte. The techniqueis inherently a concentration technique, where the analytes concentrateinto pure zones migrating with the same speed. The technique iscurrently less popular than the stacking methods described above becauseof the need for several choices of leading and trailing electrolytes,and the ability to separate only cationic or anionic species during aseparation process.

The heart of the DNA sequencing process is the remarkably selectiveelectrophoretic separation of DNA or oligonucleotide fragments. It isremarkable because each fragment is resolved and differs by onlynucleotide. Separations of up to 1000 fragments (1000 bp) have beenobtained. A further advantage of sequencing with cleavable tags is asfollows. There is no requirement to use a slab gel format when DNAfragments are separated by polyacrylamide gel electrophoresis whencleavable tags are employed. Since numerous samples are combined (4 to2000) there is no need to run samples in parallel as is the case withcurrent dye-primer or dye-terminator methods (i.e., ABI373 sequencer).Since there is no reason to run parallel lanes, there is no reason touse a slab gel. Therefore, one can employ a tube gel format for theelectrophoretic separation method. Grossman (Grossman et al., Genet.Anal. Tech. Appl. 9:9, 1992) have shown that considerable advantage isgained when a tube gel format is used in place of a slab gel format.This is due to the greater ability to dissipate Joule heat in a tubeformat compared to a slab gel which results in faster run times (by50%), and much higher resolution of high molecular weight DNA fragments(greater than 1000 nt). Long reads are critical in genomic sequencing.Therefore, the use of cleavable tags in sequencing has the additionaladvantage of allowing the user to employ the most efficient andsensitive DNA separation method which also possesses the highestresolution.

4. Microfabricated Devices

Capillary electrophoresis (CE) is a powerful method for DNA sequencing,forensic analysis, PCR product analysis and restriction fragment sizing.CE is far faster than traditional slab PAGE since with capillary gels afar higher potential field can be applied. However, CE has the drawbackof allowing only one sample to be processed per gel. The method combinesthe faster separations times of CE with the ability to analyze multiplesamples in parallel. The underlying concept behind the use ofmicrofabricated devices is the ability to increase the informationdensity in electrophoresis by miniaturizing the lane dimension to about100 micrometers. The electronics industry routinely usesmicrofabrication to make circuits with features of less than one micronin size. The current density of capillary arrays is limited the outsidediameter of the capillary tube. Microfabrication of channels produces ahigher density of arrays. Microfabrication also permits physicalassemblies not possible with glass fibers and links the channelsdirectly to other devices on a chip. Few devices have been constructedon microchips for separation technologies. A gas chromatograph (Terry etal., IEEE Trans. Electron Device, ED-26:1880, 1979) and a liquidchromatograph (Manz et al., Sens. Actuators B1:249, 1990) have beenfabricated on silicon chips, but these devices have not been widelyused. Several groups have reported separating fluorescent dyes and aminoacids on microfabricated devices (Manz et al., J. Chromatography593:253, 1992, Effenhauser et al., Anal. Chem. 65:2637, 1993). RecentlyWoolley and Mathies (Woolley and Mathies, Proc. Natl. Acad. Sci.91:11348, 1994) have shown that photolithography and chemical etchingcan be used to make large numbers of separation channels on glasssubstrates. The channels are filled with hydroxyethyl cellulose (HEC)separation matrices. It was shown that DNA restriction fragments couldbe separated in as little as two minutes.

D. Cleavage of Tags

As described above, different linker designs will confer cleavability(“lability”) under different specific physical or chemical conditions.Examples of conditions which serve to cleave various designs of linkerinclude acid, base, oxidation, reduction, fluoride, thiol exchange,photolysis, and enzymatic conditions.

Examples of cleavable linkers that satisfy the general criteria forlinkers listed above will be well known to those in the art and includethose found in the catalog available from Pierce (Rockford, Ill.).Examples include:

ethylene glycobis(succinimidylsuccinate) (EGS), an amine reactivecross-linking reagent which is cleavable by hydroxylamine (1 M at 37° C.for 3-6 hours);

disuccinimidyl tartarate (DST) and sulfo-DST, which are amine reactivecross-linking reagents, cleavable by 0.015 M sodium periodate;

bis[2-(succinimidyloxycarbonyloxy)ethyl]sulfone (BSOCOES) andsulfo-BSOCOES, which are amine reactive cross-linking reagents,cleavable by base (pH 11.6);

1,4-di-[3′-(2′-pyridyldithio(propionamido))butane (DPDPB), apyridyldithiol crosslinker which is cleavable by thiol exchange orreduction;

N-[4-(p-azidosalicylamido)-butyl]-3′-(2′-pyridydithio)propionamide(APDP), a pyridyldithiol crosslinker which is cleavable by thiolexchange or reduction;

bis-[beta-4-(azidosalicylamido)ethyl]-disulfide, a photoreactivecrosslinker which is cleavable by thiol exchange or reduction;

N-succinimidyl-(4-azidophenyl)-1,3′dithiopropionate (SADP), aphotoreactive crosslinker which is cleavable by thiol exchange orreduction;

sulfosuccinimidyl-2-(7-azido-4-methylcoumarin-3-acetamide)ethyl-1,3′-dithiopropionate:(SAED), a photoreactive crosslinker which is cleavable by thiol exchangeor reduction;

sulfosuccinimidyl-2-(m-azido-o-nitrobenzamido)-ethyl-1,3′dithiopropionate(SAND), a photoreactive crosslinker which is cleavable by thiol exchangeor reduction.

Other examples of cleavable linkers and the cleavage conditions that canbe used to release tags are as follows. A silyl linking group can becleaved by fluoride or under acidic conditions. A 3-, 4-, 5-, or6-substituted-2-nitrobenzyloxy or 2-, 3-, 5-, or6-substituted-4-nitrobenzyloxy linking group can be cleaved by a photonsource (photolysis). A 3-, 4-, 5-, or 6-substituted-2-alkoxyphenoxy or2-, 3-, 5-, or 6-substituted-4-alkoxyphenoxy linking group can becleaved by Ce(NH₄)₂(NO₃)₆ (oxidation). A NCO₂ (urethane) linker can becleaved by hydroxide (base), acid, or LiAlH₄ (reduction). A 3-pentenyl,2-butenyl, or 1-butenyl linking group can be cleaved by O₃, O_(S)O₄/IO₄⁻, or KMnO₄ (oxidation). A 2-[3-, 4-, or 5-substituted-furyl]oxy linkinggroup can be cleaved by O₂, Br₂, MeOH, or acid.

Conditions for the cleavage of other labile linking groups include:t-alkyloxy linking groups can be cleaved by acid; methyl(dialkyl)methoxyor 4-substituted-2-alkyl-1,3-dioxlane-2-yl linking groups can be cleavedby H₃O⁺; 2-silylethoxy linking groups can be cleaved by fluoride oracid; 2-(X)-ethoxy (where X=keto, ester amide, cyano, NO₂, sulfide,sulfoxide, sulfone) linking groups can be cleaved under alkalineconditions; 2-, 3-, 4-, 5-, or 6-substituted-benzyloxy linking groupscan be cleaved by acid or under reductive conditions; 2-butenyloxylinking groups can be cleaved by (Ph₃P)₃RhCl(H), 3-, 4-, 5-, or6-substituted-2-bromophenoxy linking groups can be cleaved by Li, Mg, orBuLi; methylthiomethoxy linking groups can be cleaved by Hg²⁺;2-(X)-ethyloxy (where X=a halogen) linking groups can be cleaved by Znor Mg; 2-hydroxyethyloxy linking groups can be cleaved by oxidation(e.g., with Pb(OAc)₄).

Preferred linkers are those that are cleaved by acid or photolysis.Several of the acid-labile linkers that have been developed for solidphase peptide synthesis are useful for linking tags to MOIs. Some ofthese linkers are described in a recent review by Lloyd-Williams et al.(Tetrahedron 49:11065-11133, 1993). One useful type of linker is basedupon p-alkoxybenzyl alcohols, of which two, 4-hydroxymethylphenoxyaceticacid and 4-(4-hydroxymethyl-3-methoxyphenoxy)butyric acid, arecommercially available from Advanced ChemTech (Louisville, Ky.). Bothlinkers can be attached to a tag via an ester linkage to thebenzylalcohol, and to an amine-containing MOI via an amide linkage tothe carboxylic acid. Tags linked by these molecules are released fromthe MOI with varying concentrations of trifluoroacetic acid. Thecleavage of these linkers results in the liberation of a carboxylic acidon the tag. Acid cleavage of tags attached through related linkers, suchas 2,4-dimethoxy-4′-(carboxymethyloxy)-benzhydrylamine (available fromAdvanced ChemTech in FMOC-protected form), results in liberation of acarboxylic amide on the released tag.

The photolabile linkers useful for this application have also been forthe most part developed for solid phase peptide synthesis (seeLloyd-Williams review). These linkers are usually based on2-nitrobenzylesters or 2-nitrobenzylamides. Two examples of photolabilelinkers that have recently been reported in the literature are4-(4-(1-Fmoc-amino)ethyl)-2-methoxy-5-nitrophenoxy)butanoic acid (Holmesand Jones, J. Org. Chem. 60:2318-2319, 1995) and3-(Fmoc-amino)-3-(2-nitrophenyl)propionic acid (Brown et al., MolecularDiversity 1:4-12, 1995). Both linkers can be attached via the carboxylicacid to an amine on the MOI. The attachment of the tag to the linker ismade by forming an amide between a carboxylic acid on the tag and theamine on the linker. Cleavage of photolabile linkers is usuallyperformed with UV light of 350 nm wavelength at intensities and timesknown to those in the art. Examples of commercial sources of instrumentsfor photochemical cleavage are Aura Industries Inc. (Staten Island,N.Y.) and Agrenetics (Wilmington, Mass.). Cleavage of the linkersresults in liberation of a primary amide on the tag. Examples ofphotocleavable linkers include nitrophenyl glycine esters, exo- andendo-2-benzonorborneyl chlorides and methane sulfonates, and3-amino-3(2-nitrophenyl) propionic acid. Examples of enzymatic cleavageinclude esterases which will cleave ester bonds, nucleases which willcleave phosphodiester bonds, proteases which cleave peptide bonds, etc.

E. Detection of Tags

Detection methods typically rely on the absorption and emission in sometype of spectral field. When atoms or molecules absorb light, theincoming energy excites a quantized structure to a higher energy level.The type of excitation depends on the wavelength of the light. Electronsare promoted to higher orbitals by ultraviolet or visible light,molecular vibrations are excited by infrared light, and rotations areexcited by microwaves. An absorption spectrum is the absorption of lightas a function of wavelength. The spectrum of an atom or molecule dependson its energy level structure. Absorption spectra are useful foridentification of compounds. Specific absorption spectroscopic methodsinclude atomic absorption spectroscopy (AA), infrared spectroscopy (IR),and UV-vis spectroscopy (uv-vis).

Atoms or molecules that are excited to high energy levels can decay tolower levels by emitting radiation. This light emission is calledfluorescence if the transition is between states of; the same spin, andphosphorescence if the transition occurs between states of differentspin. The emission intensity of an analyte is linearly proportional toconcentration (at low concentrations), and is useful for quantifying theemitting species. Specific emission spectroscopic methods include atomicemission spectroscopy (AES), atomic fluorescence spectroscopy (AFS),molecular laser-induced fluorescence (LIF), and X-ray fluorescence(XRF).

When electromagnetic radiation passes through matter, most of theradiation continues in its original direction but a small fraction isscattered in other directions. Light that is scattered at the samewavelength as the incoming light is called Rayleigh scattering. Lightthat is scattered in transparent solids due to vibrations (phonons) iscalled Brillouin scattering. Brillouin scattering is typically shiftedby 0.1 to 1 wave number from the incident light. Light that is scattereddue to vibrations in molecules or optical phonons in opaque solids iscalled Raman scattering. Raman scattered light is shifted by as much as4000 wavenumbers from the incident light. Specific scatteringspectroscopic methods include Raman spectroscopy.

IR spectroscopy is the measurement of the wavelength and intensity ofthe absorption of mid-infrared light by a sample. Mid-infrared light(2.5-50 μm, 4000-200 cm⁻¹) is energetic enough to excite molecularvibrations to higher energy levels. The wavelength of IR absorptionbands are characteristic of specific types of chemical bonds and IRspectroscopy is generally most useful for identification of organic andorganometallic molecules.

Near-infrared absorption spectroscopy (NIR) is the measurement of thewavelength and intensity of the absorption of near-infrared light by asample. Near-infrared light spans the 800 nm-2.5 μm (12,500-4000 cm⁻¹)range and is energetic enough to excite overtones and combinations ofmolecular vibrations to higher energy levels. NIR spectroscopy istypically used for quantitative measurement of organic functionalgroups, especially O—H, N—H, and C═O. The components and design of NIRinstrumentation are similar to uv-vis absorption spectrometers. Thelight source is usually a tungsten lamp and the detector is usually aPbS solid-state detector. Sample holders can be glass or quartz andtypical solvents are CCl₄ and CS₂. The convenient instrumentation of NIRspectroscopy makes it suitable for on-line monitoring and processcontrol.

Ultraviolet and Visible Absorption Spectroscopy (uv-vis) spectroscopy isthe measurement of the wavelength and intensity of absorption ofnear-ultraviolet and visible light by a sample. Absorption in the vacuumUV occurs at 100-200 nm; (10⁵-50,000 cm⁻¹) quartz UV at 200-350 nm;(50,000-28,570 cm⁻¹) and visible at 350-800 nm; (28,570-12,500 cm⁻¹) andis described by the Beer-Lambert-Bouguet law. Ultraviolet and visiblelight are energetic enough to promote outer electrons to higher energylevels. UV-vis spectroscopy can be usually applied to molecules andinorganic ions or complexes in solution. The uv-vis spectra are limitedby the broad features of the spectra. The light source is usually ahydrogen or deuterium lamp for uv measurements and a tungsten lamp forvisible measurements. The wavelengths of these continuous light sourcesare selected with a wavelength separator such as a prism or gratingmonochromator. Spectra are obtained by scanning the wavelength separatorand quantitative measurements can be made from a spectrum or at a singlewavelength.

Mass spectrometers use the difference in the mass-to-charge ratio (m/z)of ionized atoms or molecules to separate them from each other. Massspectrometry is therefore useful for quantitation of atoms or moleculesand also for determining chemical and structural information aboutmolecules. Molecules have distinctive fragmentation patterns thatprovide structural information to identify compounds. The generaloperations of a mass spectrometer are as follows. Gas-phase ions arecreated, the ions are separated in space or time based on theirmass-to-charge ratio, and the quantity of ions of each mass-to-chargeratio is measured. The ion separation power of a mass spectrometer isdescribed by the resolution, which is defined as R=m/delta m, where m isthe ion mass and delta m is the difference in mass between tworesolvable peaks in a mass spectrum. For example, a mass spectrometerwith a resolution of 1000 can resolve an ion with a m/z of 100.0 from anion with a m/z of 100.1.

In general, a mass spectrometer (MS) consists of an ion source, amass-selective analyzer, and an ion detector. The magnetic-sector,quadrupole, and time-of-flight designs also require extraction andacceleration ion optics to transfer ions from the source region into themass analyzer. The details of several mass analyzer designs (formagnetic-sector MS, quadrupole MS or time-of-flight MS) are discussedbelow. Single Focusing analyzers for magnetic-sector MS utilize aparticle beam path of 180, 90, or 60 degrees. The various forcesinfluencing the particle separate ions with different mass-to-chargeratios: With double-focusing analyzers, an electrostatic analyzer isadded in this type of instrument to separate particles with differencein kinetic energies.

A quadrupole mass filter for quadrupole MS consists of four metal rodsarranged in parallel. The applied voltages affect the trajectory of ionstraveling down the flight path centered between the four rods. For givenDC and AC voltages, only ions of a certain mass-to-charge ratio passthrough the quadrupole filter and all other ions are thrown out of theiroriginal path. A mass spectrum is obtained by monitoring the ionspassing through the quadrupole filter as the voltages on the rods arevaried.

A time-of-flight mass spectrometer uses the differences in transit timethrough a “drift region” to separate ions of different masses. Itoperates in a pulsed mode so ions must be produced in pulses and/orextracted in pulses. A pulsed electric field accelerates all ions into afield-free drift region with a kinetic energy of qV, where q is the ioncharge and V is the applied voltage. Since the ion kinetic energy is 0.5mV², lighter ions have a higher velocity than heavier ions and reach thedetector at the end of the drift region sooner. The output of an iondetector is displayed on an oscilloscope as a function of time toproduce the mass spectrum.

The ion formation process is the starting point for mass spectrometricanalyses. Chemical ionization is a method that employs a reagent ion toreact with the analyte molecules (tags) to form ions by either a protonor hydride transfer. The reagent ions are produced by introducing alarge excess of methane (relative to the tag) into an electron impact(EI) ion source. Electron collisions produce CH₄ ⁺ and CH₃ ⁺ whichfurther react with methane to form CH₅ ⁻ and C₂H₅ ⁺. Another method toionize tags is by plasma and glow discharge. Plasma is a hot,partially-ionized gas that effectively excites and ionizes atoms. A glowdischarge is a low-pressure plasma maintained between two electrodes.Electron impact ionization employs an electron beam, usually generatedfrom a tungsten filament, to ionize gas-phase atoms or molecules. Anelectron from the beam knocks an electron off analyte atoms or moleculesto create ions. Electrospray ionization utilizes a very fine needle anda series of skimmers. A sample solution is sprayed into the sourcechamber to form droplets. The droplets carry charge when the exit thecapillary and as the solvent vaporizes the droplets disappear leavinghighly charged analyte molecules. ESI is particularly useful for largebiological molecules that are difficult to vaporize or ionize. Fast-atombombardment (FAB) utilizes a high-energy beam of neutral atoms,typically Xe or Ar, that strikes a solid sample causing desorption andionization. It is used for large biological molecules that are difficultto get into the gas phase. FAB causes little fragmentation and usuallygives a large molecular ion peak, making it useful for molecular weightdetermination. The atomic beam is produced by accelerating ions from anion source though a charge-exchange cell. The ions pick up an electronin collisions with neutral atoms to form a beam of high energy atoms.Laser ionization (LIMS) is a method in which a laser pulse ablatesmaterial from the surface of a sample and creates a microplasma thationizes some of the sample constituents. Matrix-assisted laserdesorption ionization (MALDI) is a LIMS method of vaporizing andionizing large biological molecules such as proteins or DNA fragments.The biological molecules are dispersed in a solid matrix such asnicotinic acid. A UV laser pulse ablates the matrix which carries someof the large molecules into the gas phase in an ionized form so they canbe extracted into a mass spectrometer. Plasma-desorption ionization (PD)utilizes the decay of ²⁵²Cf which produces two fission fragments thattravel in opposite directions. One fragment strikes the sample knockingout 1-10 analyte ions. The other fragment strikes a detector andtriggers the start of data acquisition. This ionization method isespecially useful for large biological molecules. Resonance ionization(RIMS) is a method in which one or more laser beams are tuned inresonance to transitions of a gas-phase atom or molecule to promote itin a stepwise fashion above its ionization potential to create an ion.Secondary ionization (SIMS) utilizes an ion beam; such as ³He⁺, ¹⁶O⁺, or⁴⁰Ar⁺; is focused onto the surface of a sample and sputters materialinto the gas phase. Spark source is a method which ionizes analytes insolid samples by pulsing an electric current across two electrodes.

A tag may become charged prior to, during or after cleavage from themolecule to which it is attached. Ionization methods based on ion“desorption”, the direct formation or emission of ions from solid orliquid surfaces have allowed increasing application to nonvolatile andthermally labile compounds. These methods eliminate the need for neutralmolecule volatilization prior to ionization and generally minimizethermal degradation of the molecular species. These methods includefield desorption (Becky, Principles of Field Ionization and FieldDesorption Mass Spectrometry, Pergamon, Oxford, 1977), plasma desorption(Sundqvist and Macfarlane, Mass Spectrom. Rev. 4:421, 1985), laserdesorption (Karas and Hillenkamp, Anal. Chem. 60:2299, 1988; Karas etal., Angew. Chem. 101:805, 1989), fast particle bombardment (e.g., fastatom bombardment, FAB, and secondary ion mass spectrometry, SIMS, Barberet al., Anal. Chem. 54:645A, 1982), and thermospray (TS) ionization(Vestal, Mass Spectrom. Rev. 2:447, 1983). Themospray is broadly appliedfor the on-line combination with liquid chromatography. The continuousflow FAB methods (Caprioli et al., Anal. Chem. 58:2949, 1986) have alsoshown significant potential. A more complete listing of ionization/massspectrometry combinations is ion-trap mass spectrometry, electrosprayionization mass spectrometry, ion-spray mass spectrometry, liquidionization mass spectrometry, atmospheric pressure ionization massspectrometry, electron ionization mass spectrometry, metastable atombombardment ionization mass spectrometry, fast atom bombard ionizationmass spectrometry, MALDI mass spectrometry, photo-ionizationtime-of-flight mass spectrometry, laser droplet mass spectrometry,MALDI-TOF mass spectrometry, APCI mass spectrometry, nano-spray massspectrometry, nebulised spray ionization mass spectrometry, chemicalionization mass spectrometry, resonance ionization mass spectrometry,secondary ionization mass spectrometry, thermospray mass spectrometry.

The ionization methods amenable to nonvolatile biological compounds haveoverlapping ranges of applicability. Ionization efficiencies are highlydependent on matrix composition and compound type. Currently availableresults indicate that the upper molecular mass for TS is about 8000daltons (Jones and Krolik, Rapid Comm. Mass Spectrom. 1:67, 1987). SinceTS is practiced mainly with quadrapole mass spectrometers, sensitivitytypically suffers disporportionately at higher mass-to-charge ratios(m/z). Time-of-flight (TOF) mass spectrometers are commerciallyavailable and possess the advantage that the m/z range is limited onlyby detector efficiency. Recently, two additional ionization methods havebeen introduced. These two methods are now referred to asmatrix-assisted laser desorption (MALDI, Karas and Hillenkamp, Anal.Chem. 60:2299, 1988; Karas et al., Angew. Chem. 101:805, 1989) andelectrospray ionization (ESI). Both methodologies have very highionization efficiency (i.e., very high [molecular ionsproduced]/[molecules consumed]). Sensitivity, which defines the ultimatepotential of the technique, is dependent on sample-size, quantity ofions, flow rate, detection efficiency and actual ionization efficiency.

Electrospray-MS is based on an idea first proposed in the 1960s (Dole etal., J. Chem. Phys. 49:2240, 1968). Electrospray ionization (ESI) is onemeans to produce charged molecules for analysis by mass spectroscopy.Briefly, electrospray ionization produces highly charged droplets bynebulizing liquids in a strong electrostatic field. The highly chargeddroplets, generally formed in a dry bath gas at atmospheric pressure,shrink by evaporation of neutral solvent until the charge repulsionovercomes the cohesive forces, leading to a “Coulombic explosion”. Theexact mechanism of ionization is controversial and several groups haveput forth hypotheses (Blades et al., Anal. Chem. 63:2109-14, 1991;Kebarle et al., Anal. Chem. 65:A972-86, 1993; Fenn, J. Am. Soc. Mass.Spectrom. 4:524-35, 1993). Regardless of the ultimate process of ionformation, ESI produces charged molecules from solution under mildconditions.

The ability to obtain useful mass spectral data on small amounts of anorganic molecule relies on the efficient production of ions. Theefficiency of ionization for ESI is related to the extent of positivecharge associated with the molecule. Improving ionization experimentallyhas usually involved using acidic conditions. Another method to improveionization has been to use quaternary amines when possible (seeAebersold et al., Protein Science 1:494-503, 1992; Smith et al., Anal.Chem. 60:436-41, 1988).

Electrospray ionization is described in more detail as follows.Electrospray ion production requires two steps: dispersal of highlycharged droplets at near atmospheric pressure, followed by conditions toinduce evaporation. A solution of analyte molecules is passed through aneedle that is kept at high electric potential. At the end of theneedle, the solution disperses into a mist of small highly chargeddroplets containing the analyte molecules. The small droplets evaporatequickly and by a process of field desorption or residual evaporation,protonated protein molecules are released into the gas phase. Anelectrospray is generally produced by application of a high electricfield to a small flow of liquid (generally 1-10 uL/min) from a capillarytube. A potential difference of 3-6 kV is typically applied between thecapillary and counter electrode located 0.2-2 cm away (where ions,charged clusters, and even charged droplets, depending on the extent ofdesolvation, may be sampled by the MS through a small orifice). Theelectric field results in charge accumulation on the liquid surface atthe capillary terminus; thus the liquid flow rate, resistivity, andsurface tension are important factors in droplet production. The highelectric field results in disruption of the liquid surface and formationof highly charged liquid droplets. Positively or negatively chargeddroplets can be produced depending upon the capillary bias. The negativeion mode requires the presence of an electron scavenger such as oxygento inhibit electrical discharge.

A wide range of liquids can be sprayed electrostatically into a vacuum,or with the aid of a nebulizing agent. The use of only electric fieldsfor nebulization leads to some practical restrictions on the range ofliquid conductivity and dielectric constant. Solution conductivity ofless than 10⁻⁵ ohms is required at room temperature for a stableelectrospray at useful liquid flow rates corresponding to an aqueouselectrolyte solution of <10⁻⁴ M. In the mode found most useful forESI-MS, an appropriate liquid flow rate results in dispersion of theliquid as a fine mist. A short distance from the capillary the dropletdiameter is often quite uniform and on the order of 1 μm. Of particularimportance is that the total electrospray ion current increases onlyslightly for higher liquid flow rates. There is evidence that heating isuseful for manipulating the electrospray. For example, slight heatingallows aqueous solutions to be readily electrosprayed, presumably due tothe decreased viscosity and surface tension. Both thermally-assisted andgas-nebulization-assisted electrosprays allow higher liquid flow ratesto be used, but decrease the extent of droplet charging. The formationof molecular ions requires conditions effecting evaporation of theinitial droplet population. This can be accomplished at higher pressuresby a flow of dry gas at moderate temperatures (<60° C.), by heatingduring transport through the interface, and (particularly in the case ofion trapping methods) by energetic collisions at relatively lowpressure.

Although the detailed processes underlying ESI remain uncertain, thevery small droplets produced by ESI appear to allow almost any speciescarrying a net charge in solution to be transferred to the gas phaseafter evaporation of residual solvent. Mass spectrometric detection thenrequires that ions have a tractable m/z range (<4000 daltons forquadrupole instruments) after desolvation, as well as to be produced andtransmitted with sufficient efficiency. The wide range of solutesalready found to be amenable to ESI-MS, and the lack of substantialdependence of ionization efficiency upon molecular weight, suggest ahighly non-discriminating and broadly applicable ionization process.

The electrospray ion “source” functions at near atmospheric pressure.The electrospray “source” is typically a metal or glass capillaryincorporating a method for electrically biasing the liquid solutionrelative to a counter electrode. Solutions, typically water-methanolmixtures containing the analyte and often other additives such as aceticacid, flow to the capillary terminus. An ESI source has been described(Smith et al., Anal. Chem. 62:885, 1990) which can accommodateessentially any solvent system. Typical flow rates for ESI are 1-10uL/min. The principal requirement of an ESI-MS interface is to sampleand transport ions from the high pressure region into the MS asefficiently as possible.

The efficiency of ESI can be very high, providing the basis forextremely sensitive measurements, which is useful for the inventiondescribed herein. Current instrumental performance can provide a totalion current at the detector of about 2×10⁻¹² A or about 10⁷ counts/s forsingly charged species. On the basis of the instrumental performance,concentrations of as low as 10⁻¹⁰ M or about 10⁻¹⁸ mol/s of a singlycharged species will give detectable ion current (about 10 counts/s) ifthe analyte is completely ionized. For example, low attomole detectionlimits have been obtained for quaternary ammonium ions using an ESIinterface with capillary zone electrophoresis (Smith et al., Anal. Chem.59:1230, 1988). For a compound of molecular weight of 1000, the averagenumber of charges is 1, the approximate number of charge states is 1,peak width (m/z) is 1 and the maximum intensity (ion/s) is 1×10¹².

Remarkably little sample is actually consumed in obtaining an ESI massspectrum (Smith et al., Anal. Chem. 60:1948, 1988). Substantial gainsmight be also obtained by the use of array detectors with sectorinstruments, allowing simultaneous detection of portions of thespectrum. Since currently only about 10⁻⁵ of all ions formed by ESI aredetected, attention to the factors limiting instrument performance mayprovide a basis for improved sensitivity. It will be evident to those inthe art that the present invention contemplates and accommodates forimprovements in ionization and detection methodologies.

An interface is preferably placed between the separation instrumentation(e.g., gel) and the detector (e.g., mass spectrometer). The interfacepreferably has the following properties: (1) the ability to collect theDNA fragments at discreet time intervals, (2) concentrate the DNAfragments, (3) remove the DNA fragments from the electrophoresis buffersand milieu, (4) cleave the tag from the DNA fragment, (5) separate thetag from the DNA fragment, (6) dispose of the DNA fragment, (7) placethe tag in a volatile solution, (8) volatilize and ionize the tag, and(9) place or transport the tag to an electrospray device that introducesthe tag into mass spectrometer.

The interface also has the capability of “collecting” DNA fragments asthey elute from the bottom of a gel. The gel may be composed of a slabgel, a tubular gel, a capillary, etc. The DNA fragments can be collectedby several methods. The first method is that of use of an electric fieldwherein DNA fragments are collected onto or near an electrode. A secondmethod is that wherein the DNA fragments are collected by flowing astream of liquid past the bottom of a gel. Aspects of both methods canbe combined wherein DNA collected into a flowing stream which can belater concentrated by use of an electric field. The end result is thatDNA fragments are removed from the milieu under which the separationmethod was performed. That is, DNA fragments can be “dragged” from onesolution type to another by use of an electric field.

Once the DNA fragments are in the appropriate solution (compatible withelectrospray and mass spectrometry) the tag can be cleaved from the DNAfragment. The DNA fragment (or remnants thereof) can then be separatedfrom the tag by the application of an electric field (preferably, thetag is of opposite charge of that of the DNA tag). The tag is thenintroduced into the electrospray device by the use of an electric fieldor a flowing liquid.

Fluorescent tags can be identified and quantitated most directly bytheir absorption and fluorescence emission wavelengths and intensities.

While a conventional spectrofluorometer is extremely flexible, providingcontinuous ranges of excitation and emission wavelengths (l_(EX),l_(S1), l_(S2)), more specialized instruments such as flow cytometersand laser-scanning microscopes require probes that are excitable at asingle fixed wavelength. In contemporary instruments, this is usuallythe 488-nm line of the argon laser.

Fluorescence intensity per probe molecule is proportional to the productof e and QY. The range of these parameters among fluorophores of currentpractical importance is approximately 10,000 to 100,000 cm⁻¹M⁻¹ for εand 0.1 to 1.0 for QY. When absorption is driven toward saturation byhigh-intensity illumination, the irreversible destruction of the excitedfluorophore (photobleaching) becomes the factor limiting fluorescencedetectability. The practical impact of photobleaching depends on thefluorescent detection technique in question.

It will be evident to one in the art that a device (an interface) may beinterposed between the separation and detection steps to permit thecontinuous operation of size separation and tag detection (in realtime). This unites the separation methodology and instrumentation withthe detection methodology and instrumentation forming a single device.For example, an interface is interposed between a separation techniqueand detection by mass spectrometry or potentiostatic amperometry.

The function of the interface is primarily the release of the (e.g.,mass spectrometry) tag from analyte. There are several representativeimplementations of the interface. The design of the interface isdependent on the choice of cleavable linkers. In the case of light orphoto-cleavable linkers, an energy or photon source is required. In thecase of an acid-labile linker, a base-labile linker, or a disulfidelinker, reagent addition is required within the interface. In the caseof heat-labile linkers, an energy heat source is required. Enzymeaddition is required for an enzyme-sensitive linker such as a specificprotease and a peptide linker, a nuclease and a DNA or RNA linker, aglycosylase, HRP or phosphatase and a linker which is unstable aftercleavage (e.g., similar to chemiluminescent substrates). Othercharacteristics of the interface include minimal band broadening,separation of DNA from tags before injection into a mass spectrometer.Separation techniques include those based on electrophoretic methods andtechniques, affinity techniques, size retention (dialysis), filtrationand the like.

It is also possible to concentrate the tags (or nucleic acid-linker-tagconstruct), capture electrophoretically, and then release into alternatereagent stream which is compatible with the particular type ofionization method selected. The interface may also be capable ofcapturing the tags (or nucleic acid-linker-tag construct) on microbeads,shooting the bead(s) into chamber and then preforming laserdesorption/vaporization. Also it is possible to extract in flow intoalternate buffer (e.g., from capillary electrophoresis buffer intohydrophobic buffer across a permeable membrane). It may also bedesirable in some uses to deliver tags into the mass spectrometerintermittently which would comprise a further function of the interface.Another function of the interface is to deliver tags from multiplecolumns into a mass spectrometer, with a rotating time slot for eachcolumn. Also, it is possible to deliver tags from a single column intomultiple MS detectors, separated by time, collect each set of tags for afew milliseconds, and then deliver to a mass spectrometer.

The following is a list of representative vendors for separation anddetection technologies which may be used in the present invention.Hoefer Scientific Instruments (San Francisco, Calif.) manufactureselectrophoresis equipment (Two Step™, Poker Face™ II) for sequencingapplications. Pharmacia Biotech (Piscataway, N.J.) manufactureselectrophoresis equipment for DNA separations and sequencing(PhastSystem for PCR-SSCP analysis, MacroPhor System for DNAsequencing). Perkin Elmer/Applied Biosystems Division (ABI, Foster City,Calif.) manufactures semi-automated sequencers based on fluorescent-dyes(ABI373 and ABI377). Analytical Spectral Devices (Boulder, Colo.)manufactures UV spectrometers. Hitachi Instruments (Tokyo, Japan)manufactures Atomic Absorption spectrometers. Fluorescencespectrometers, LC and GC Mass Spectrometers, NMR spectrometers, andUV-VIS Spectrometers. PerSeptive Biosystems (Framingham, Mass.) producesMass Spectrometers (Voyager™ Elite). Bruker Instruments Inc. (ManningPark, Mass.) manufactures FTIR Spectrometers (Vector 22), FT-RamanSpectrometers, Time of Flight Mass Spectrometers (Reflex II™), Ion TrapMass Spectrometer (Esquire™) and a Maldi Mass Spectrometer. AnalyticalTechnology Inc. (ATI, Boston, Mass.) makes Capillary Gel Electrophoresisunits, UV detectors, and Diode Array Detectors. Teledyne ElectronicTechnologies (Mountain View, Calif.) manufactures an Ion Trap MassSpectrometer (3DQ Discovery™ and the 3DQ Apogee™). Perkin Elmer/AppliedBiosystems Division (Foster City, Calif.) manufactures a Sciex MassSpectrometer (triple quadrupole LC/MS/MS, the API 100/300) which iscompatible with electrospray. Hewlett-Packard (Santa Clara, Calif.)produces Mass Selective Detectors (HP 5972A), MALDI-TOF MassSpectrometers (HP G2025A), Diode Array Detectors, CE units, HPLC units(HP1090) as well as UV Spectrometers. Finnigan Corporation (San Jose,Calif.) manufactures mass spectrometers (magnetic sector (MAT 95 S™),quadrapole spectrometers (MAT 95 SQ™) and four other related massspectrometers). Rainin (Emeryville, Calif.) manufactures HPLCinstruments.

The methods and compositions described herein permit the use of cleavedtags to serve as maps to particular sample type and nucleotide identity.At the beginning of each sequencing method, a particular (selected)primer is assigned a particular unique tag. The tags map to either asample type, a dideoxy terminator type (in the case of a Sangersequencing reaction) or preferably both. Specifically, the tag maps to aprimer type which in turn maps to a vector type which in turn maps to asample identity. The tag may also may map to a dideoxy terminator type(ddTTP, ddCTP, ddGTP, ddATP) by reference into which dideoxynucleotidereaction the tagged primer is placed. The sequencing reaction is thenperformed and the resulting fragments are sequentially separated by sizein time.

The tags are cleaved from the fragments in a temporal frame and measuredand recorded in a temporal frame. The sequence is constructed bycomparing the tag map to the temporal frame. That is, all tag identitiesare recorded in time after the sizing step and related become related toone another in a temporal frame. The sizing step separates the nucleicacid fragments by a one nucleotide increment and hence the related tagidentities are separated by a one nucleotide increment. By foreknowledgeof the dideoxy-terminator or nucleotide map and sample type, thesequence is readily deduced in a linear fashion.

A genetic fingerprinting system of the present invention consists of, ingeneral, a sample introduction device, a device to separate the taggedsamples of interest, a splitting device to deviate a variable amount ofthe sample to a fraction collector, a device to cleave the tags from thesamples of interest, a device for detecting the tag, and a softwareprogram to analyze the data collected and display it in a differentialdisplay mode. It will be evident to one of ordinary skill in the artwhen in possession of the present disclosure that this generaldescription may have many variances for each of the components listed.As best seen in FIG. 15, an exemplary genetic fingerprinting system 10of the present invention consists of a sample introduction device 12, aseparation device 14 that separates the samples by high-performanceliquid chromatography (HPLC), a splitting device 13, a fractioncollector 15, a photocleavage device 16 to cleave the tags from thesamples of interest, a detection device 18 that detects the tags bymeans of an electrochemical detector, and a data processing device 20with a data analysis software program that analyzes the results from thedetection device. Each component is discussed in more detail below.

The sample introduction device 12 automatically takes a measured aliquot22 of the PCR products generated in the genetic fingerprinting procedureand delivers it through a conventional tube 24 to the separation device14 (generally an HPLC). The sample introduction device 12 of theexemplary embodiment consists of a temperature-controlled autosampler 26that can accommodate micro-titer plates. The autosampler 26 istemperature controlled to maintain the integrity of the nucleic acidsamples generated and is able to inject 25 μl or less of sample.Manufacturers of this type of sample introduction device 12 are, forexample, Gilson (Middleton, Wis.).

The sample introduction device is operatively connected in series to theseparation device 14 by the conventional tube 24. The PCR products inthe measured aliquot 22 received in the separation device 14 areseparated temporally by high performance liquid chromatography toprovide separated DNA fragments. The high-performance liquidchromatograph may have an isocratic, binary, or quaternary pump(s) 27and can be purchased from multiple manufacturers (e.g., Hewlett Packard(Palo Alto, Calif.) HP 1100 or 1090 series, Beckman Instruments Inc.(800-742-2345), Bioanalytical Systems, Inc. (800845-4246), ESA, Inc.(508) 250-700), Perkin-Elmer Corp. (800-762-4000), Varian Instruments(800-926-3000), Waters Corp. (800-254-4752)).

The separation device 14 includes an analytical HPLC column 28 suitablefor use to separate the oligonucleotides. The column 28 is an analyticalHPLC, for example, non-porous polystyrene divinylbenzene (2.2 μmparticle size) solid support modified which can operate within a pHrange of 2 to 12, pressures of up to 3000 psi and a temperature range of10 to 70° C. A temperature-control device (e.g. a column oven) (notshown) may be used to control the temperature of the column. Suchtemperature-control devices are known in the art, and may be obtainedfrom, for example, Rainin Instruments (subsidiary of Varian Instrument,Palo Alto, Calif.). A suitable column 28 is available under thecommercial name of DNAsep® and is available from Serasep (San Jose,Calif.). Other suitable analytical HPLC columns are available from othermanufacturers (e.g., Hewlett Packard (Palo Alto, Calif.), BeckmanIndustries (Brea, Calif.), Waters Corp. (Milford, Mass.), and Supelco(Bellefonte, Pa.).

The separation device 14 in the illustrated embodiment incorporates thesample splitter 13, and the sample splitter is connected to the flowingstream of the sample. The sample splitter 13 is adapted to divert in aconventional manner variable amounts of sample to the fraction collector15 either for further analysis or storage. The fraction collector 15must be able to accommodate small volumes, have temperature control tolow temperatures, and have adjustable sampling times. Manufacturers ofin-line splitters include Upchurch (Oak Harbor, Wash.).

The fraction collector 15 is attached to the HPLC/LC device via astream-splitter line 29. Fraction collectors 15 permit the collection ofspecific peaks, DNAs, RNAs, and nucleic acid fragments or molecules ofinterest into tubes, wells of microtiter plates, or containers.Additionally, fraction collectors 15 can collect all or part of a set ofnucleic acid fragments separated by HPLC or LC. Manufacturers offraction collectors include Gilson (Middleton, Wis.), and Isco (Lincoln,Nebr.). The use of a fraction collector 15 in this technology providesconsiderable substantial advantages over gel based systems. For example,it is possible to directly clone nucleic acids fragments recovered byHPLC or LC methods. In addition, it is possible to amplify nucleic acidsfragments recovered by HPLC or LC methods by PCR. These two methodspermit the rapid identification of nucleic acid fragments of interest ona sequence level. Both methods are tedious and ineffective when used inconjunction with gel-based systems.

In the illustrated embodiment, the fraction collector 15 is anindividual component of the genetic fingerprinting system 10. In analternate embodiment (not shown), the fraction collector 15 isincorporated in the sample introduction device 12. Accordingly, thestream-splitter line 32 directs the diverted sample from the samplesplitter 13 back to the sample introduction device 12.

A stream of the separated DNA fragments (e.g., sequencing reactionproducts) flows through a conventional tube 30 from the separationdevice 14 downstream of the sample splitter 13 to the cleavage device16. Each of the DNA fragments is labeled with a unique cleavable (e.g.,photocleavable) tag. The flowing stream of separated DNA fragments passthrough or past the cleaving device 16, where the tag is removed fordetection (e.g., by mass spectrometry or with an electrochemicaldetector). In the exemplary embodiment, the cleaving device 16 is aphotocleaving unit such that flowing stream of sample is exposed toselected light energy and wave length. In one embodiment, the sampleenters the photocleaving unit 16 and is exposed to the selected lightsource for a selected duration of time. In an alternate embodiment, theflowing stream of sample is carried adjacent to the light source along apath that provides a sufficient exposure to the light energy to cleavethe tags from the separated DNA fragments.

A photocleaving unit is available from Supelco (Bellefonte, Pa.).Photocleaving can be performed at multiple wavelengths with amercury/xenon arc lamp. The wavelength accuracy is about 2 nm with abandwidth of 10 nm. The area irradiated is circular and typically of anarea of 10-100 square centimeters. In alternate embodiments, othercleaving devices, which cleave by acid, base, oxidation, reduction,fluoride, thiol exchange, photolysis, or enzymatic conditions, can beused to remove the tags from the separated DNA fragments.

After the cleaving device 16 cleaves the tags from the separated DNAfragments, the tags flow through a conventional tube 32 to the detectiondevice 18 for detection of each tag. Detection of the tags can be basedupon the difference in electrochemical potential between each of thetags used to label each kind of DNA generated in the PCR step. Theelectrochemical detector 18 can operate on either coulometric oramperometric principles. The preferred electromechanical detector 18 isthe coulometric detector, which consists of a flow-through orporous-carbon graphite amperometric detector where the column elandpasses through the electrode resulting in 100% detection efficiency. Tofully detect each component, an array of 16 coulometric detectors eachheld at a different potential (generally at 60 mV increments) isutilized. Examples of manufacturers of this type of detector are ESA(Bedford, Mass.) and Bioanalytical Systems Inc. (800-845-4246).

In an alternate embodiment illustrated schematically in FIG. 16, thesample introduction device 12, the separating device 14, and thecleavage device 16 are serially connected as discussed above formaintaining the flow of sample. The cleavage device 16 is connected to adetection device 18 which is a mass spectrometer 40 or the like thatdetects the tags based upon the difference in molecular weight betweeneach of the tags used to label each kind of DNA generated in the PCRstep. The best detector based upon differences in mass is the massspectrometer. For this use, the mass spectrometer 40 will typically havean atmospheric pressure ionization (API) interface with eitherelectrospray or chemical ionization, a quadrupole mass analyzer, and amass range of at least 50 to 2600 m/z. Examples of manufacturers of asuitable mass spectrometer are: Hewlett Packard (Palo Alto, Calif.) HP1100 LC/MSD, Hitachi Instruments (San Jose, Calif.), M-1200H LC/MS,Perkin Elmer Corporation, Applied Biosystems Division (Foster City,Calif.) API 100 LC/MS or API 300 LC/MS/MS, Finnigan Corporation (SanJose, Calif.) LCQ, MAT 95 S, Bruker Analytical Systems, Inc. (Billerica,Mass.) APEX, BioAPEX, and ESQUIRE and Micromass (U.K.).

The detection device 18 is electrically connected to a data processorand analyzer 20 that receives data from the detection device. The dataprocessor and analyzer 20 includes a software program that identifiesthe detected tag. The data processor and analyzer 230 in alternateembodiments is operatively connected to the injection device 12, theseparation device 14, the fraction collector 15, and/or the cleavingdevice 16 to control the different components of the geneticfingerprinting system 10.

The software package maps the electrochemical signature of a given tagto a specific primer, and a retention time. Software generated nucleicacid profiles are then compared (length to length, fragment to fragment)and the results are reported to the user. The software will highlightboth similarities and differences in the nucleic acid fragment profiles.The software will also be able to direct the collection of specificnucleic acid fragments by the fraction collector 15.

The software package maps the m/z signature of a given tag to a specificprimer, and a retention time. Software generated nucleic acid profilesare then compared (length to length, fragment to fragment) and theresults are reported to the user. The software will highlight bothsimilarities and differences in the nucleic acid fragment profiles. Thesoftware will also be able to direct the collection of specific nucleicacid fragments by the fraction collector.

The system 18 in accordance with the present invention is provided byoperatively interconnecting the system's multiple components.Accordingly, one or more system components, such as the sampleintroducing device 12 and the detecting device 18 that, are in operationin a lab can be combined with the system's other components, (e.g., theseparating device 14, cleaving device 16, and the data processor andanalyzer 20 in order to equip the lab with the DNA sequencing system 10of the present invention.

Another embodiment of the present invention provides a differentialdisplay system which consists of, in general, a sample introductiondevice, a device to separate the tagged samples of interest, a splittingdevice to deviate a variable amount of the sample to a fractioncollector, a unit to cleave the tags from the samples of interest, adevice for detecting the tag, and a software program to analyze the datacollected and display it in a differential display mode. It will beevident to one of ordinary skill in possession of the present disclosurethat the general description may have many variances for each of thecomponents listed. The differential display system of an exemplaryembodiments of the present invention consists of similar componentsillustrated in FIG. 15, including the sample introduction device 12, theseparation device 14 for separating the samples by high-performanceliquid chromatography (HPLC), the splitting device 13, the fractioncollector 15, the photocleavage device 16 to cleave the tags from thesamples of interest, the detection device 18 for detection of the tagsby electrochemistry, and the data processor and analyzer 20 with asoftware program. Each component is discussed in more detail below.

In the differential display system, the sample introduction device 12automatically takes a measured aliquot 22 of the PCR product generatedin the differential display procedure and delivers it through aconventional tube 24 to the separation device 14 (generally an HPLC).The sample introduction device 12 of the exemplary embodiment consistsof a temperature-controlled autosampler 26 that can accommodatemicro-titer plates. The autosampler 26 must be temperature controlled tomaintain the integrity of the nucleic acid samples generated and be ableto inject 25 μl or less of sample. Manufacturers of this type of productare represented, for example, by Gilson (Middleton, Wis.).

The sample introduction device is operatively connected in series to theseparation device by the conventional tube 24. The PCR products in themeasured aliquot 22 received in the separation device 14 are separatedtemporally by high performance liquid chromatography to provideseparated DNA fragments. The high-performance liquid chromatograph mayhave an isocratic, binary, or quaternary pump(s) 27 and can be purchasedfrom multiple manufacturers (e.g., Hewlett Packard (Palo Alto, Calif.)HP 1100 or 1090 series, Analytical Technology Inc. (Madison, Wis.),Perkin Elmer, Waters, etc.). The separation device 14 includes ananalytical HPLC column 28 suitable for use to separate theoligonucleotides. The column 28 is an analytical HPLC, for example,non-porous polystyrene divinylbenzene (2.2 μm particle size) solidsupport modified which can operate within a pH range of 2 to 12,pressures of up to 3000 psi and a temperature range of 10 to 70° C. Atemperature-control device (e.g., a column oven) (not shown) may be usedto control the temperature of the column. Such temperature-controldevices are known in the art, and may be obtained from, for example,Rainin Instruments (subsidiary of Varian Instrument, Palo Alto, Calif.).A suitable column 28 is available under the commercial name of DNAsep®and is available from Serasep (San Jose, Calif.). Other suitableanalytical HPLC columns are available from other manufacturers (e.g.,Hewlett Packard (Palo Alto, Calif.) (Beckman Industries (Brea, Calif.),Waters Corp. (Milford, Mass.), and Supelco (Bellefonte, Pa.).

In the illustrated embodiment, the fraction collector 15 is anindividual component of the differential display system 10 that iscoupled to the system's other components. In an alternate embodiment,the fraction collector 15 is incorporated in the sample introductiondevice 12. Accordingly, the stream-splitter line 32 directs the divertedsample from the sample splitter 13 back to the sample introductiondevice 12.

The separation device 14 in the illustrated embodiment incorporates thesample splitter 13 that is connected to the flowing stream of thesample. The sample splitter 13 is adapted to divert in a conventionalmanner variable amounts of sample to the fraction collector 15 eitherfor further analysis or storage. The fraction collector 15 must be ableto accommodate small volumes, have temperature control to lowtemperatures, and have adjustable sampling times. Manufacturers ofin-line splitters include Upchurch (Oak Harbor, Wash.).

A stream of the separated DNA fragments flow through a conventional tube30 from the separation device 14 downstream of the sample splitter 113to the cleavage device 16. Each of the PCR products is labeled with aunique cleavable (e.g., photocleavable) tag. The flowing stream ofseparated DNA fragments pass through or past the cleaving device 16where the tag is removed for detection by electrochemical detection. Inthe exemplary embodiment, the cleaving device 16 is a photocleaving unitsuch that flowing stream of sample is exposed to selected light energy.In one embodiment, the sample enters the photocleaving unit 16 and isexposed to the selected light source for a selected duration of time. Inan alternate embodiment, the flowing stream of sample is carried in asuitable tube portion or the like adjacent to the light source along apath that provides a sufficient exposure to the light source to cleavethe tags from the separated DNA fragments.

A photocleaving unit is available from Supelco (Bellefonte, Pa.).Photocleaving can be performed at multiple wavelengths with amercury/xenon arc lamp. The wavelength accuracy is about 2 nm with abandwidth of 10 nm. The area irradiated is circular and typically of anarea of 10-100 square centimeters. In alternate embodiments, othercleaving devices, which cleave by acid, base, oxidation, reduction,fluoride, thil exchange, photolysis, or enzymatic conditions, can beused to remove the tags from the separated DNA fragments.

After the cleaving device 16 cleaves the tags from the separated DNAfragments, the tags flow through a conventional tube 32 to the detectiondevice 18 for detection of each tag. Detection of the tags is based uponthe difference in electrochemical potential between each of the tagsused to label each kind of DNA generated in the PCR step. Theelectrochemical detector 18 can operate on either coulometric oramperometric principles. The preferred electromechanical detector 18 isthe coulometric detector, which consists of a flow-through orporous-carbon graphite amperometric detector where the column eluentpasses through the electrode resulting in 100% detection efficiency. Tofully detect each component, an array of 16 coulometric detectors eachheld at a different potential (generally at 60 mV increments) isutilized. The manufacturers of this type of detector include ESA(Bedford, Mass.) and Bioanalytical Systems Inc. (800-845-4246).

In an alternate embodiment of the differential display systemillustrated schematically in FIG. 16, the sample introduction device 12,the separating device 14, and the cleavage device 16 are seriallyconnected as discussed above for maintaining the flow of sample. Thecleavage device 16 is connected to a detection device 18 that detectsthe tags based upon the difference in molecular weight between each ofthe tags used to label each kind of DNA generated in the PCR step. Thebest detector based upon differences in mass is the mass spectrometer40. For this use, the mass spectrometer will typically have anatmospheric pressure ionization (API) interface with either electrosprayor chemical ionization, a quadrupole mass analyzer, and a mass range ofat least 50 to 2600 m/z. Examples of manufacturers of a suitable massspectrometer are: Hewlett Packard (Palo Alto, Calif.) HP 1100 LC/MSD,Hitachi Instruments (San Jose, Calif.), M-1200H LC/MS, JEOL. USA, Inc.(Peabody, Mass.), Perkin Elmer Corporation, Applied Biosystems Division(Foster City, Calif.) API 100 LC/MS or API 300 LC/MS/MS, FinniganCorporation (San Jose, Calif.) LCQ, MAT 95 S, MAT 95 S Q, MAT 900 S, MAT900 S Q, and SSQ 7000, Bruker Analytical Systems, Inc. (Billerica,Mass.) APEX, BioAPEX, and ESQUIRE.

The detection device 18 is electrically connected to a data processorand analyzer 20 that receives data from the detection device. The dataprocessor and analyzer 20 includes a software program that identifiesthe detected tag and its position in the DNA sequence. The dataprocessor and analyzer 20 in alternate embodiments is operativelyconnected to the injection device 12, the separation device 14, thefraction collector 15, and/or the cleaving device 16 to control thedifferent components of the differential display system.

The software package maps the signature of a given tag to a specificprimer, and a retention time. Software generated nucleic acid profilesare then compared (length to length, fragment to fragment) and theresults are reported to the user. The software will highlight bothsimilarities and differences in the nucleic acid fragment profiles. Thesoftware will also be able to direct the collection of specific nucleicacid fragments by the fraction collector 15.

The software package maps the m/z signature of a given tag to a specificprimer, and a retention time. Software generated nucleic acid profilesare then compared (length to length, fragment to fragment) and theresults are reported to the user. The software highlights bothsimilarities and differences in the nucleic acid fragment profiles. Thesoftware is also able to direct the collection of specific nucleic acidfragments by the fraction collector.

The differential display system is provided by operativelyinterconnecting the system's multiple components. Accordingly, one ormore system components, such as the sample introducing device 12 and thedetecting device 18 that are in operation in a lab can be combined withthe system's other components, e.g., the separating device 14, cleavingdevice 16, and the data processor and analyzer 20, in order to equip thelab with a system in accordance with the present invention.

Single nucleotide extension assay, oligo-ligation assay oroligonucleotide probe based assay systems of the present inventionconsist of, in general, a sample introduction device, a device toseparate the tagged samples of interest, a device to cleave the tagsfrom the samples of interest, a device for detecting the tag, and asoftware program to analyze the data collected. It will be evident toone of ordinary skill in the art when in possession of the presentdisclosure that the general description may have many variances for eachof the components listed. As best seen in FIG. 17, (need Figure #) apreferred single-nucleotide extension assay, oligo-ligation assay oroligonucleotide-probe based assay system 200 consists of a sampleintroduction device 212, a separation device 214 that separates thesamples by high-performance liquid chromatography, a cleaving device 216to cleave the tags from the samples of interest, a detection device 218of the tags by mass spectrometry, and a data processor and analyzer 220which includes a software program. Each component is discussed in moredetail below.

The sample introduction device 212 automatically takes a measuredaliquot 222 of the nucleic acid fragment generated by a variety ofmethods (PCR, ligations, digestion, nucleases, etc.) and delivers itthrough a conventional tube 224 to the separation device 214 (generallyan HPLC). The sample introduction device 212 of the exemplary embodimentconsists of a temperature-controlled autosampler 226 that canaccommodate micro-titer plates. The autosampler 226 must be temperaturecontrolled to maintain the integrity of the nucleic acid samplesgenerated and be able to inject 25 μl or less of sample. Manufacturersof this product are represented, for example, by Gilson (MiddletonWis.).

The sample introduction device is operatively connected in series to theseparation device by the conventional tube 224. The nucleic acidproducts (which may be produced by PCR, ligation reactions, digestion,nucleases, etc.) in the measured aliquot 222 receive in the separationdevice 214 are separated temporally by high performance liquidchromatography. The high-performance liquid chromatograph may have anisocratic, binary, or quaternary pump(s) 227 and can be purchased frommultiple manufacturers (e.g., Hewlett Packard (Palo Alto, Calif.) HP1100 or 1090 series, Beckman Instruments Inc. (800-742-2345),Bioanalytical Systems, Inc. (800-845-4246), ESA, Inc. (508) 250-700),Perkin-Elmer Corp. (800-762-4000), Varian Instruments (800-926-3000),Waters Corp. (800-254-4752)).

The separations device 214 includes an analytical HPLC column 228suitable for use to separate the nucleic acid fragments. The column 228is an analytical HPLC, for example, non-porous polystyrenedivinylbenzene (2.2 μm particle size) solid support which can operatewithin a pH range of 2 to 12, pressures of up to 3000 psi and atemperature range of 10 to 70° C. A temperature-control device (e.g., acolumn oven) (not shown) may be used to control the temperature of thecolumn. Such temperature-control devices are known in the art, and maybe obtained from, for example, Rainin Instruments (subsidiary of VarianInstrument, Palo Alto, Calif.). A suitable column 228 is available underthe commercial name of DNAsep® and is available from Serasep (San Jose,Calif.). A wide variety of HPLC columns 228 can be used for thisparticular technological unit since single-base pair resolution is notnecessarily required. Other suitable analytical HPLC columns areavailable from other manufacturers (e.g., Hewlett Packard (Palo Alto,Calif.), Beckman Instruments, Inc. (Brea, Calif.), and Waters Corp.(Milford, Mass.)).

A stream of the separated DNA fragments (e.g., sequencing reactionproduct) flows through a conventional tube 230 from the separationdevice 214 to the cleavage device 216. Each of the DNA fragments islabeled with a unique cleavable (e.g., photocleavable) tag. The flowingstream of separated DNA fragments pass through or past the cleavingdevice 216 where the tag is removed for detection by mass spectrometryor with a electrochemical detector. The photocleaving unit is availablefrom Supelco (Bellefonte, Pa.). Photocleaving can be performed atmultiple wavelengths with a mercury/xenon arc lamp. The wavelengthaccuracy is about 2 nm with a bandwidth of 10 nm. The area irradiated iscircular and typically of an area of 10-100 square centimeters. Inalternate embodiments, other cleaving devices, which cleave by acid,base, oxidation, reduction, fluoride, thiol exchange, photolysis, orenzymatic conditions, can be used to remove the tags from the separatedDNA fragments.

After the cleaving device 216 cleaves the tags from the separated DNAfragments, the tags flow through a conventional tube 232 to thedetection device 218 for detection of each tag. Detection of the tagscan be based upon the difference in molecular weight between each of thetags used to label each kind of DNA generated in the various assaysteps. The best detector based upon differences in mass is the massspectrometer. For this use, the mass spectrometer will typically have anatmospheric pressure ionization (API) interface with either electrosprayor chemical ionization, a quadrupole mass analyzer, and a mass range ofat least 50 to 2600 m/z. Examples of manufacturers of a suitable massspectrometer are: Hewlett Packard (Palo Alto, Calif.) HP 1100 LC/MSD,Hitachi Instruments (San Jose, Calif.) M-1200H LC/MS, Perkin ElmerCorporation, Applied Biosystems Division (Foster City, Calif.) API 100LC/MS or API 300 LC/MS/MS, Finnigan Corporation (San Jose, Calif.) LCQ,Bruker Analytical Systems, Inc. (Billerica, Mass.), ESQUIRE, andMicromers (U.K).

In an alternate embodiment illustrated schematically in FIG. 18, thesample introduction device 212, the separating device 214, and thecleavage device 216 are serially connected as discussed above formaintaining the flow of sample. The cleavage device 216 is connected toa detection device 218, which is an electrochemical detector 240 thatdetects the tags based upon the difference in electrochemical potentialbetween each of the tags used to label each kind of DNA generated in thesequencing reaction step. The electrochemical detector 240 of theexemplary embodiment can operate on either coulometric or amperometricprinciples. The preferred electrochemical detector 240 is thecoulometric detector, which consists of a flow-through or porous-carbongraphite amperometric detector where the column eluent passes throughthe electrode resulting in 100% detection efficiency. To fully detecteach component, an array of 16 coulometric detectors each held at adifferent potential (generally at 60 mV increments) is utilized.Examples of manufacturers of this type of detector are ESA (Bedford,Mass.) and Bioanalytical Systems Inc. (800-845-4246). Additionalmanufacturers of electrochemical detectors can be found in the list ofother manufacturers found below.

The electrochemical detector 240 is electrically connected to the dataprocessor and analyzer 220 with the software package discussed above.The software package maps the detected property (e.g., the mass orelectrochemical signature) of a given tag to a specific sample ID. Thesoftware will be able to identify the nucleic acid fragment of interestand load the ID information into respective databases.

The DNA analysis systems described herein have numerous advantages overthe traditional gel based systems. One of the principal advantages isthat these systems may be fully automated. By utilizing an HPLC basedseparation system, samples can be automatically injected into the HPLCwhere as gel based systems require manual loading. There is also asignificant time savings found in the set-up time (no gel forms toclean, no gel to pour), and the analysis time (greater than 4 hours fora large gel versus much shorter times (5 minutes to an hour) for an HPLCanalysis Additionally, there is a sample throughput advantage. Byutilizing the tags described in this invention, many samples can beanalyzed in one batch (potentially 384 samples/lane) whereas thegel-based analyses are limited to the 4 fluorophores available or onesample/lane. The gels used are inherently delicate and can easily breakor contain an air bubble or other flaw rendering the whole gel orseveral lanes useless. HPLC columns are rugged and, when purchasedpre-packed, are free of packing defects creating a consistent, generallyuniform separation path. The HPLC systems also lend towards betterquality assurance in that internal standards can be utilized due to thereproducibility of the HPLC columns. Gel quality is inconsistent bothbetween gels as well as within a gel making use of standards nearlyimpossible. Finally, both the mass spectrometry and electrochemicaldetectors are more sensitive than the detectors utilized in the gelbased systems allowing for lower limits of detection and analysis ofless sample which would be useful for non-PCR based analyses.

Tagged Probes in Array-Based Assays

Arrays with covalently attached oligonucleotides have been made used toperform DNA sequence analysis by hybridization (Southern et al.,Genomics 13: 1008, 1992; Drmanac et al., Science 260: 1649, 1993),determine expression profiles, screen for mutations and the like. Ingeneral, detection for these assays uses fluorescent or radioactivelabels. Fluorescent labels can be identified and quantitated mostdirectly by their absorption and fluorescence emission wavelengths andintensity. A microscope/camera setup using a fluorescent light source isa convenient means for detecting fluorescent label. Radioactive labelsmay be visualized by standard autoradiography, phosphor image analysisor CCD detector. For such labels the number of different reactions thatcan be detected at a single time is limited. For example, the use offour fluorescent molecules, such as commonly employed in DNA sequenceanalysis, limits anaylsis to four samples at a time. Essentially,because of this limitation, each reaction must be individually assessedwhen using these detector methods.

A more advantageous method of detection allows pooling of the samplereactions on at least one array and simultaneous detection of theproducts. By using a tag, such as the ones described herein, having adifferent molecular weight or other physical attribute in each reaction,the entire set of reaction products can be harvested together andanalyzed.

As noted above, the methods described herein are applicable for avariety of purposes. For example, the arrays of oligonucleotides may beused to control for quality of making arrays, for quantitation orqualitative analysis of nucleic acid molecules, for detecting mutations,for determining expression profiles, for toxicology testing, and thelike.

1. Probe Quantitation or Typing

In this embodiment, oligonucleotides are immobilized per element in anarray where each oligonucleotide in the element is a different orrelated sequence. Preferably, each element possesses a known or relatedset of sequences. The hybridization of a labeled probe to such an arraypermits the characterization of a probe and the identification andquantification of the sequences contained in a probe population.

A generalized assay format that may be used in the particularapplications discussed below is a sandwich assay format. In this format,a plurality of oligonucleotides of known sequence are immobilized on asolid substrate. The immobilized oligonucleotide is used to capture anucleic acid (e.g., RNA, rRNA, a PCR product, fragmented DNA) and then asignal probe is hybridized to a different portion of the captured targetnucleic acid.

Another generalized assay format is a secondary detection system. Inthis format, the arrays are used to identify and quantify labelednucleic acids that have been used in a primary binding assay. Forexample, if an assay results in a labeled nucleic acid, the identity ofthat nucleic acid can be determined by hybridization to an array. Theseassay formats are particularly useful when combined with cleavable massspectometry tags.

2. Mutation Detection

Mutations involving a single nucleotide can be identified in a sample byscanning techniques, which are suitable to identify previously unknownmutations, or by techniques designed to detect, distinguish, orquantitate known sequence variants. Several scanning techniques formutation detection have been developed based on the observation thatheteroduplexes of mismatched complementary DNA strands, derived fromwild type and mutant sequences, exhibit an abnormal migratory behavior.

The methods described herein may be used for mutation screening. Onestrategy for detecting a mutation in a DNA strand is by hybridization ofthe test sequence to target sequences that are wild-type or mutantsequences. A mismatched sequence has a destabilizing effect on thehybridization of short oligonucleotide probes to a target sequence (seeWetmur, Crit. Rev. Biochem. Mol. Biol., 26:227, 1991). The test nucleicacid source can be genomic DNA, RNA, cDNA, or amplification of any ofthese nucleic acids. Preferably, amplification of test sequences isfirst performed, followed by hybridization with short oligonucleotideprobes immobilized on an array. An amplified product can be scanned formany possible sequence variants by determining its hybridization patternto an array of immobilized oligonucleotide probes.

A label, such as described herein, is generally incorporated into thefinal amplification product by using a labeled nucleotide or by using alabeled primer. The amplification product is denatured and hybridized tothe array. Unbound product is washed off and label bound to the array isdetected by one of the methods herein. For example, when cleavable massspectrometry tags are used, multiple products can be simultaneouslydetected.

3. Expression Profiles/differential Display

Mammals, such as human beings, have about, 100,000 different genes intheir genome, of which only a small fraction, perhaps 15%, are expressedin any individual cell. Differential display techniques permit theidentification of genes specific for individual cell types. Briefly, indifferential display, the 3′ terminal portions of mRNAs are amplifiedand identified on the basis of size. Using a primer designed to bind tothe 5′ boundary of a poly(A) tail for reverse transcription, followed byamplification of the cDNA using upstream arbitrary sequence primers,mRNA sub-populations are obtained.

As disclosed herein, a high throughput method for measuring theexpression of numerous genes (e.g., 1-2000) is provided. Within oneembodiment of the invention, methods are provided for analyzing thepattern of gene expression from a selected biological sample, comprisingthe steps of (a) amplifying cDNA from a biological sample using one ormore tagged primers, wherein the tag is correlative with a particularnucleic acid probe and detectable by non-fluorescent spectrometry orpotentiometry, (b) hybridizing amplified fragments to an array ofoligonucleotides as described herein, (c) washing away non-hybridizedmaterial, and (d) detecting the tag by non-fluorescent spectrometry orpotentiometry, and therefrom determining the pattern of gene expressionof the biological sample. Tag-based differential display, especiallyusing cleavable mass spectometry tags, on solid substrates allowscharacterization of differentially expressed genes.

4. Single Nucleotide Extension Assay

The primer extension technique may be used for the detection of singlenucleotide changes in a nucleic acid template (Sokolov, Nucleic AcidsRes., 18:3671, 1989). The technique is generally applicable to detectionof any single base mutation (Kuppuswamy et al., Proc. Natl, Acad. Sci.USA, 88:1143-1147, 1991). Briefly, this method first hybridizes a primerto a sequence adjacent to a known single nucleotide polymorphism. Theprimed DNA is then subjected to conditions in which a DNA polymeraseadds a labeled dNTP, typically a ddNTP, if the next base in the templateis complementary to the labeled nucleotide in the reaction mixture. In amodification, cDNA is first amplified for a sequence of interestcontaining a single-base difference between two alleles. Each amplifiedproduct is then analyzed for the presence, absence, or relative amountsof each allele by annealing a primer that is 1 base 5′ to thepolymorphism and extending by one labeled base (generally adideoxynucleotide). Only when the correct base is available in thereaction will a base to incorporated at the 3′-end of the primer.Extension products are then analyzed by hybridization to an array ofoligonucleotides such that a non-extended product will not hybridize.

Briefly, in the present invention, each dideoxynucleotide is labeledwith a unique tag. Of the four reaction mixtures, only one will add adideoxy-terminator on to the primer sequence. If the mutation ispresent, it will be detected through the unique tag on thedideoxynucleotide after hybridization to the array. Multiple mutationscan be simultaneously determined by tagging the DNA primer with a uniquetag as well. Thus, the DNA fragments are reacted in four separatereactions each including a different tagged dideoxyterminator, whereinthe tag is correlative with a particular dideoxynucleotide anddetectable by non-fluorescent spectrometry, or potentiometry. The DNAfragments are hybridized to an array and non-hybridized material iswashed away. The tags are cleaved from the hybridized fragments anddetected by the respective detection technology (e.g., massspectrometry, infrared spectrometry, potentiostatic amperometry orUV/visible spectrophotometry). The tags detected can be correlated tothe particular DNA fragment under investigation as well as the identityof the mutant nucleotide.

5. Oligonucleotide Ligation Assay

The oligonucleotide ligation assay (OLA). (Landegen et al., Science241:487, 1988) is used for the identification of known sequences in verylarge and complex genomes. The principle of OLA is based on the abilityof ligase to covalently join two diagnostic oligonucleotides as theyhybridize adjacent to one another on a given DNA target. If thesequences at the probe junctions are not perfectly based-paired, theprobes will not be joined by the ligase. When tags are used, they areattached to the probe, which is ligated to the amplified product. Aftercompletion of OLA, fragments are hybridized to an array of complementarysequences, the tags cleaved and detected by mass spectrometry.

Within one embodiment of the invention methods are provided fordetermining the identity of a nucleic acid molecule, or for detecting aselecting nucleic acid molecule, in, for example a biological sample,utilizing the technique of oligonucleotide ligation assay. Briefly, suchmethods generally comprise the steps of performing amplification on thetarget DNA followed by hybridization with the 5′ tagged reporter DNAprobe and a 5′ phosphorylated probe. The sample is incubated with T4 DNAligase. The DNA strands with ligated probes are captured on the array byhybridization to an array, wherein non-ligated products do nothybridize. The tags are cleaved from the separated fragments, and thenthe tags are detected by the respective detection technology (e.g., massspectrometry, infrared spectrophotometry, potentiostatic amperometry orUV/visible spectrophotometry.

6. Other Assays

The methods described herein may also be used to genotype oridentification of viruses or microbes. For example, F+ RNA coliphagesmay be useful candidates as indicators for enteric virus contamination.Genotyping by nucleic acid amplification and hybridization methods arereliable, rapid, simple, and inexpensive alternatives to serotyping(Kafatos et. al., Nucleic Acids Res. 7:1541, 1979). Amplificationtechniques and nucleic aid hybridization techniques have beensuccessfully used to classify a variety of microorganisms including E.coli (Feng, Mol. Cell Probes 7:151, 1993), rotavirus (Sethabutr et. al.,J. Med Virol. 37:192, 1992), hepatitis C virus (Stuyver et. al., J. GenVirol. 74:1093, 1993), and herpes simplex virus (Matsumoto et. al., J.Virol. Methods 40:119, 1992).

Genetic alterations have been described in a variety of experimentalmammalian and human neoplasms and represent the morphological basis forthe sequence of morphological alterations observed in carcinogenesis(Vogelstein et al., NEJM 319:525, 1988). In recent years with the adventof molecular biology techniques, allelic losses on certain chromosomesor mutation of tumor suppressor genes as well as mutations in severaloncogenes (e.g., c-myc, c-jun, and the ras family) have been the moststudied entities. Previous work (Finkelstein et al., Arch Surg. 128:526,1993) has identified a correlation between specific types of pointmutations in the K-ras oncogene and the stage at diagnosis in colorectalcarcinoma. The results suggested that mutational analysis could provideimportant information of tumor aggressiveness, including the pattern andspread of metastasis. The prognostic value of TP53 and K-ras-2mutational analysis in stage III carconoma of the colon has morerecently been demonstrated (Pricolo et al., Am. J. Surg. 171:41, 1996).It is therefore apparent that genotyping of tumors and pre-cancerouscells, and specific mutation detection will become increasinglyimportant in the treatment of cancers in humans.

Tagged Probes in Array-Based Assays

The tagged biomolecules as disclosed herein may be used to interrogate(untagged) arrays of biomolecules. Preferred arrays of biomolculescontain a solid substrate comprising a surface, where the surface is atleast partially covered with a layer of poly(ethylenimine) (PEI). ThePEI layer comprises a plurality of discrete first regions abutted andsurrounded by a contiguous second region. The first regions are definedby the presence of a biomolecule and PEI, while the second region isdefined by the presence of PEI and the substantial absence of thebiomolecule. Preferably, the substrate is a glass plate or a siliconwafer. However, the substrate may be, for example, quartz, gold,nylon-6,6, nylon or polystyrene, as well as composites thereof, asdescribed above.

The PEI coating preferably contains PEI having a molecular weightranging from 100 to 100,000. The PEI coating may be directly bonded tothe substrate using, for example, silylated PEI. Alternatively, areaction product of a bifunctional coupling agent may be disposedbetween the substrate surface and the PEI coating, where the reactionproduct is covalently bonded to both the surface and the PEI coating,and secures the PEI coating to the surface. The bifunctional couplingagent contains a first and a second reactive functional group, where thefirst reactive functional group is, for example, atri(O—C₁-C₅alkyl)silane, and the second reactive functional group is,for example, an epoxide, isocyanate, isothiocyanate and anhydride group.Preferred bifunctional coupling agents include2-(3,4-epoxycyclohexyl)ethyltrimethoxysilane;3,4-epoxybutyltrimethoxysilane; 3-isocyanatopropyltriethoxysilane,3-(triethoxysilyl)-2-methylpropylsuccinic anhydride and3-(2,3-epoxypropoxy)propyltrimethoxysilane.

The array of the invention contains first, biomolecule-containingregions, where each region has an area within the range of about 1,000square microns to about 100,000 square microns. In a preferredembodiment, the first regions have areas that range from about 5,000square microns to about 25,000 square microns.

The first regions are preferably substantially circular, where thecircles have an average diameter of about 10 microns to 200 microns.Whether circular or not, the boundaries of the first regions arepreferably separated from one another (by the second region) by anaverage distance of at least about 25 microns, however by not more thanabout 1 cm (and preferably by no more than about 1,000 microns). In apreferred array, the boundaries of neighboring first regions areseparated by an average distance of about 25 microns to 100 microns,where that distance is preferably constant throughout the array, and thefirst regions are preferably positioned in a repeating geometric patternas shown in the FIGures attached hereto. In a preferred repeatinggeometric pattern, all neighboring first regions are separated byapproximately the same distance (about 25 microns to about 100 microns).

In preferred arrays, there are from 10 to 50 first regions on thesubstrate. In another embodiment, there are 50 to 400 first regions on asubstrate. In yet another preferred embodiment, there are 400 to 800first regions on the substrate.

The biomolecule located in the first regions is preferably a nucleicacid polymer. A preferred nucleic acid polymer is an oligonucleotidehaving from about 15 to about 50 nucleotides. The biomolecule may beamplification reaction products having from about 50 to about 1,000nucleotides.

In each first region, the biomolecule is preferably present at anaverage concentration ranging from 10⁵ to 10⁹ biomolecules per 2,000square microns of a first region. More preferably, the averageconcentration of biomolecule ranges from 10⁷ to 10⁹ biomolecules per2,000 square microns. In the second region, the biomolecule ispreferably present at an average concentration of less than 10³biomolecules per 2,000 square microns of said second region, and morepreferably at an average concentration of less than 10² biomolecules per2,000 square microns. Most preferably, the second regions does notcontain any biomolecule.

The chemistry used to adhere the layer of PEI to the substrate depends,in substantial part, upon the chemical identity of the substrate. Theprior art provides numerous examples of suitable chemistries that mayadhere PEI to a solid support. For example, when the substrate isnylon-6,6, the PEI coating may be applied by the methods disclosed inVan Ness, J. et al. Nucleic Acids Res. 19:3345-3350, 1991 and PCTInternational Publication WO 94/00600, both of which are incorporatedherein by reference. When the solid support is glass or silicon,suitable methods of applying a layer of PEI are found in, e.g.,Wasserman, B. P. Biotechnology and Bioengineering XXII:271-287, 1980;and D'Souza, S. F. Biotechnology Letters 8:643-648, 1986.

Preferably, the PEI coating is covalently attached to the solidsubstrate. When the solid substrate is glass or silicon, the PEI coatingmay be covalently bound to the substrate using silylating chemistry. Forexample, PEI having reactive siloxy endgroups is commercially availablefrom Gelest, Inc. (Tullytown, Pa.). Such reactive PEI may be contactedwith a glass slide or silicon wafer, and after gentle agitation, the PEIwill adhere to the substrate. Alternatively, a bifunctional silylatingreagent may be employed. According to this process, the glass or siliconsubstrate is treated with the bifunctional silylating reagent to providethe substrate with a reactive surface. PEI is then contacted with thereactive surface, and covalently binds to the surface through thebifunctional reagent.

The biomolecules being placed into the array format are originallypresent in a so-called “arraying solution”. In order to placebiomolecule in discrete regions on the PEI-coated substrate, thearraying solution preferably contains a thickening agent at aconcentration of about 35 vol % to about 80 vol % based on the totalvolume of the composition, a biomolecule which is preferably anoligonucleotide at a concentration ranging from 0.001 μg/mL to 10 μg/mL,and water.

The concentration of the thickening agent is 35% V/V to 80% V/V forliquid thickening agents such as glycerol. The preferred concentrationof thickening agent in the composition depends, to some extent, on thetemperature at which the arraying is performed. The lower the arrayingtemperature, the lower the concentration of thickening agent that needsto be used. The combination of temperature and liquid thickening agentconcentration control permits arrays to be made on most types of solidsupports (e.g., glass, wafers, nylon 6/6, nylon membranes, etc.).

The presence of a thickening agent has the additional benefit ofallowing the concurrent presence of low concentrations of various othermaterials to be present in combination with the biomolecule. For.example 0.001% V/V to 1% V/V of detergents may be present in thearraying solution. This is useful because PCR buffer contains a smallamount of Tween-20 or NP-40, and it is frequently desirable to arraysample nucleic acids directly from a PCR vial without prior purificationof the amplicons. The use of a thickening agent permits the presence ofsalts (for example NaCl, KCl, or MgCl₂), buffers (for example Tris),and/or chelating reagents (for example EDTA) to also be present in thearraying solution. The use of a thickening agent also has the additionalbenefit of permitting the use of cross-linking reagents and/or organicsolvents to be present in the arraying solution. As commerciallyobtained, cross-linking reagents are commonly dissolved in organicsolvent such as DMSO, DMF, NMP, methanol, ethanol and the like. Commonlyused organic solvents can be used in arraying solutions of the inventionat levels of 0.05% to 20% (V/V) when thickening agents are used.

In general, the thickening agents impart increased viscosity to thearraying solution. When a proper viscosity is achieved in the arrayingsolution, the first drop is the substantially the same size as, forexample, the 100th drop deposited. When an improper viscosity is used inthe arraying solution, the first drops deposited are significantlylarger than latter drops which are deposited. The desired viscosity isbetween those of pure water and pure glycerin.

The biomolecule in the array may be a nucleic acid polymer or analogthereof, such as PNA, phosphorothioates and methylphosphonates. Nucleicacid refers to both ribonucleic acid and deoxyribonucleic acid. Thebiomolecule may comprise unnatural and/or synthetic bases. Thebiomolecule may be single or double stranded nucleic acid polymer.

A preferred biomolecule is an nucleic acid polymer, which includesoligonucleotides (up to about 100 nucleotide bases) and polynucleotides(over about 100 bases). A preferred nucleic acid polymer is formed from15 to 50 nucleotide bases. Another preferred nucleic acid polymer has 50to 1,000 nucleotide bases. The nucleic acid polymer may be a PCRproduct, PCR primer, or nucleic acid duplex, to list a few examples.However, essentially any nucleic acid type can be covalently attached toa PEI-coated surface when the nucleic acid contains a primary amine, asdisclosed below. The typical concentration of nucleic acid polymer inthe arraying solution is 0.001-10 μg/mL, preferably 0.01-1 μg/mL, andmore preferably 0.05-0.5 μg/mL.

Preferred nucleic acid polymers are “amine-modified” in that they havebeen modified to contain a primary amine at the 5′-end of the nucleicacid polymer, preferably with one or more methylene (—CH₂—) groupsdisposed between the primary amine and the nucleic acid portion of thenucleic acid polymer. Six is a preferred number of methylene groups.Amine-modified nucleic acid polymers are preferred because they can becovalently coupled to a solid support through the 5′-amine group. PCRproducts can be arrayed using 5′-hexylamine modified PCR primers.Nucleic acid duplexes can be arrayed after the introduction of amines bynick translation using aminoallyl-dUTP (Sigma, St. Louis, Mo.). Aminescan be introduced into nucleic acids by polymerases such as terminaltransferase with amino allyl-dUTP or by ligation of shortamine-containing nucleic acid polymers onto nucleic acids by ligases.

Preferably, the nucleic acid polymer is activated prior to be contactedwith the PEI coating. This can be conveniently accomplished by combiningamine-functionalized nucleic acid polymer with a multi-functionalamine-reactive chemical such as trichlorotriazine. When the nucleic acidpolymer contains a 5′-amine group, that 5′-amine can be reacted withtrichlorotriazine, also known as cyanuric chloride (Van Ness et al.,Nucleic Acids Res. 19(2):3345-3350, 1991) Preferably, an excess ofcyanuric chloride is added to the nucleic acid polymer solution, where a10- to 1000-fold molar excess of cyanuric chloride over the number ofamines in the nucleic acid polymer in the arraying solution ispreferred. In this way, the majority of amine-terminated nucleic acidpolymers have reacted with one molecule of trichlorotriazine, so thatthe nucleic acid polymer becomes terminated with dichlorotriazine.

Preferably, the arraying solution is buffered using a common buffer suchas sodium phosphate, sodium borate, sodium carbonate, or Tris HCl. Apreferred pH range for the arraying solution is 7 to 9, with a preferredbuffer being freshly prepared sodium borate at pH 8.3 to pH 8.5. Toprepare a typical arraying solution, hexylamine-modified nucleic acidpolymer is placed in 0.2 M sodium borate, pH 8.3, at 0.1 μg/mL, to atotal volume of 50 μl. Ten μl of a 15 mg/mL solution of cyanuricchloride is then added, and the reaction is allowed to proceed for 1hour at 25 C. with constant agitation. Glycerol (Gibco Brl®, GrandIsland, N.Y.) is added to a final concentration of 56%.

The biomolecular arraying solutions may be applied to the PEI coating byany of the number of techniques currently used in microfabrication. Forexample, the solutions may be placed into an ink jet print head, andejected from such a head onto the coating.

A preferred approach to delivering biomolecular solution onto the PEIcoating employs a modified spring probe. Spring probes are availablefrom several vendors including Everett Charles (Pomona, Calif.),Interconnect Devices Inc. (Kansas City, Kans.) and Test ConnectionsInc., (Upland, Calif.). In order for the commercially available springprobes as described above to satisfactorily function as liquiddeposition devices according to the present invention, approximately{fraction (1/1000)}th to {fraction (5/1000)}th of an inch of metalmaterial must be removed from the tip of the probe. The process mustresult in a flat surface which is perpendicular to the longitudinal axisof the spring probe. The removal of approximately {fraction (1/1000)}thto {fraction (5/1000)}th of an inch of material from the bottom of thetip is preferred and can be accomplished easily with a very fine grainedwet stone. Specific spring probes which are commercially available andmay be modified to provide a planar tip as described above include theXP54 probe manufactured by Ostby Barton (a division of Everett Charles(Pomona, Calif.)); the SPA 25P probe manufactured by Everett Charles(Pomona, Calif.) and 43-P fluted spring probe from Test ConnectionsInc., (Upland, Calif.).

The arraying solutions as described above may be used directly in anarraying process. That is, the activated nucleic acid polymers need notbe purified away from unreacted cyanuric chloride prior to the printingstep. Typically the reaction which attaches the activated nucleic acidto the solid support is allowed to proceed for 1 to 20 hours at 20 to 50C. Preferably, the reaction time is 1 hour at 25 C.

The arrays as described herein are particularly useful in conductinghybridization assays, for example, using CMST labeled probes. However,in order to perform such assays, the amines on the solid support must becapped prior to conducting the hybridization step. This may beaccomplished by reacting the solid support with 0.1-2.0 M succinicanhydride. The preferred reaction conditions are 1.0 M succinicanhydride in 70% m-pyrol and 0.1 M sodium borate. The reaction typicallyis allowed to occur for 15 minutes to 4 hours with a preferred reactiontime of 30 minutes at 25 C. Residual succinic anhydride is removed witha 3× water wash.

The solid support is then incubated with a solution containing 0.1-5 Mglycine in 0.1-10.0 M sodium borate at pH 7-9. This step “caps” anydichloro-triazine which may be covalently bound to the PEI surface byconversion into monochlorotriazine. The preferred conditions are 0.2 Mglycine in 0.1 M sodium borate at pH 8.3. The solid support may then bewashed with detergent-containing solutions to remove unbound materials,for example, trace NMP. Preferably, the solid support is heated to 95 C.in 0.01 M NaCl, 0.05 M EDTA and 01 M Tris pH 8.0 for 5 minutes. Thisheating step removes non-covalently attached nucleic acid polymers, suchas PCR products. In the case where double strand nucleic acid arearrayed, this step also has the effect of converting the double strandto single strand form (denaturation).

The arrays are may be interrogated by probes (e.g., oligonucleotides,nucleic acid fragments, PCR products, etc.) which may be tagged with,for example CMST tags as described herein, radioisotopes, fluorophoresor biotin. The methods for biotinylating nucleic acids are well known inthe art and are adequately described by Pierce (Avidin-Biotin Chemistry:A Handbook, Pierce Chemical Company, 1992. Rockford Ill.). Probes aregenerally used at 0.1 ng/mI, to 10/μg/mL in standard hybridizationsolutions that include GuSCN, GuHCl, formamide, etc. (see Van Ness andChen, Nucleic Acids Res., 19:5143-5151, 1991).

To detect the hybridization event (i.e., the presence of the biotin),the solid support is incubated with streptavidin/horseradish peroxidaseconjugate. Such enzyme conjugates are commercially available from, forexample, Vector Laboratories (Burlingham, Calif.). The streptavidinbinds with high affinity to the biotin molecule bringing the horseradishperoxidase into proximity to the hybridized probe. Unboundstreptavidin/horseradish peroxidase conjugate is washed away in a simplewashing step. The presence of horseradish peroxidase enzyme is thendetected using a precipitating substrate in the presence of peroxide andthe appropriate buffers.

A blue enzyme product deposited on a reflective surface such as a waferhas a many-fold lower level of detection (LLD) compared to that expectedfor a calorimetric substrate. Furthermore, the LLD is vastly differentfor different colored enzyme products. For example, the LLD for4-methoxynapthol (which produces a precipitated blue product) per 50 μMdiameter spot is approximately 1000 molecules, whereas a redprecipitated substrate gives an LLD about 1000-fold higher at 1,000,000molecules per 50 μM diameter spot. The LLD is determined byinterrogating the surface with a microscope (such as the Axiotechmicroscope commercially available from Zeiss) equipped with a visiblelight source and a CCD camera (Princeton Instruments, Princeton, N.J.).An image of approximately 10,000 μM×10,000 μM can be scanned at onetime.

In order to use the blue colorimetric detection scheme, the surface mustbe very clean after the enzymatic reaction and the wafer or slide mustbe scanned in a dry state. In addition, the enzymatic reaction must bestopped prior to saturation of the reference spots. For horseradishperoxidase this is approximately 2-5 minutes.

It is also possible to use chemiluminescent substrates for alkalinephosphatase or horesradish peroxidase (HRP), or fluoroescence substratesfor HRP or alkaline phosphatase. Examples include the dioxetanesubstrates for alkaline phosphatase available from Perkin Elmer orAttophos HRP substrate from JBL Scientific (San Luis Obispo, Calif.).

The following examples are offered by way of illustration, and not byway of limitation.

Unless otherwise stated, chemicals as used in the examples may beobtained from Aldrich Chemical Company, Milwaukee, Wis. The followingabbreviations, with the indicated meanings, are used herein:

ANP-=3-(Fmoc-amino)-3-(2-nitrophenyl)propionic acid

NBA=4-(Fmoc-aminomethyl)-3-nitrobenzoic acid

HATU=O-7-azabenzotriazol-1-yl-N,N,N′,N′-tetramethyluroniumhexafluorophosphate

DIEA=diisopropylethylamine

MCT=monochlorotriazine

NMM=4-methylmorpholine

NMP=N-methylpyrrolidone

ACT357=ACT357 peptide synthesizer from Advanced ChemTech, Inc.,Louisville, Ky.

ACT=Advanced ChemTech, Inc., Louisville, Ky.

NovaBiochem=CalBiochem-NovaBiochem International, San Diego, Calif.

TFA=Trifluoroacetic acid

Tfa=Trifluoroacetyl

iNIP=N-Methylisonipecotic acid

Tfp=Tetrafluorophenyl

DIAEA=2-(Diisopropylamino)ethylamine

MCT=monochlorotriazene

5′-AH-ODN=5′-aminohexyl-tailed oligodeoxynucleotide

EXAMPLES Example 1 Preparation of Avid Labile Linkers for Use inCleavable-MW-Identifier Sequencing

A. Synthesis of Pentafluorophenyl Esters of Chemically Cleavable MassSpectroscopy Tags, to Liberate Tags with Carboxyl Amide Termini

FIG. 1 shows the reaction scheme.

Step A. TentaGel S AC resin (compound II; available from ACT; 1 eq.) issuspended with DMF in the collection vessel of the ACT357 peptidesynthesizer (ACT). Compound 1 (3 eq.), HATU (3 eq.) and DIEA (7.5 eq.)in DMF are added and the collection vessel shaken for 1 hr. The solventis removed and the resin washed with NMP (2×), MeOH (2×), and DMF (2×).The coupling of I to the resin and the wash steps are repeated, to givecompound III.

Step B. The resin (compound III) is mixed with 25% piperidine in DMF-andshaken for 5 min. The resin is filtered, then mixed with 25% piperidinein DMF and shaken for 10 min. The solvent is removed, the resin washedwith NMP (2×), MeOH (2×), and DMF (2×), and used directly in step C.

Step C. The deprotected resin from step B is suspended in DMF and to itis added an FMOC-protected amino acid, containing amine functionality inits side chain (compound IV, e.g., alpha-N-FMOC-3-(3-pyridyl)-alanine,available from Synthetech, Albany, Oreg.; 3 eq.), HATU (3 eq.), and DIEA(7.5 eq.) in DMF. The vessel is shaken for 1 hr. The solvent is removedand the resin washed with NMP (2×), MeOH (2×), and DMF (2×). Thecoupling of IV to the resin and the wash steps are repeated, to givecompound V.

Step D. The resin (compound V) is treated with piperidine as describedin step B to remove the FMOC group. The deprotected resin is thendivided equally by the ACT357 from the collection vessel into 16reaction vessels.

Step E. The 16 aliquots of deprotected resin from step D are suspendedin DMF. To each reaction vessel is added the appropriate carboxylic acidVI₁₋₁₆ (R₁₋₁₆CO₂H; 3 eq.), HATU (3 eq.), and DIEA (7.5 eq.) in DMF. Thevessels are shaken for 1 hr. The solvent is removed and the aliquots ofresin washed with NMP (2×), MeOH (2×), and DMF (2×). The coupling ofVI₁₋₁₆ to the aliquots of resin and the wash steps are repeated, to givecompounds VII₁₋₁₆.

Step F. The aliquots of resin (compounds VII₁₋₁₆) are washed with CH₂Cl₂(3×). To each of the reaction vessels is added 1% TFA in CH₂Cl₂ and thevessels shaken for 30 min. The solvent is filtered from the reactionvessels into individual tubes. The aliquots of resin are washed withCH₂Cl₂ (2×) and MeOH (2×) and the filtrates combined into the individualtubes. The individual tubes are evaporated in vacuo, providing compoundsVIII₁₋₁₆.

Step G. Each of the free carboxylic acids VIII₁₋₁₆ is dissolved in DMF.To each solution is added pyridine (1.05 eq.), followed bypentafluorophenyl trifluoroacetate (1.1 eq.). The mixtures are stirredfor 45 min. at room temperature. The solutions are diluted with EtOAc,washed with 1 M aq. citric acid (3×) and 5% aq. NaHCO₃ (3×), dried overNa₂SO₄, filtered, and evaporated in vacuo, providing compounds IX₁₋₁₆.

A. Synthesis of Pentafluorophenyl Esters of Chemically Cleavable MassSpectroscopy Tags, to Liberate Tars with Carboxyl Acid Termini

FIG. 2 shows the reaction scheme.

Step A. 4-(Hydroxymethyl)phenoxybutyric acid (compound I; 1 eq.) iscombined with DIEA (2.1 eq.) and allyl bromide (2.1 eq.) in CHCl₃ andheated to reflux for 2 hr. The mixture is diluted with EtOAc, washedwith 1 N HCl (2×), pH 9.5 carbonate buffer (2×), and brine (1×), driedover Na₂SO₄, and evaporated in vacuo to give the allyl ester of compoundI.

Step B. The allyl ester of compound I from step A (1.75 eq.) is combinedin CH₂Cl₂ with an FMOC-protected amino acid containing aminefunctionality in its side chain (compound II, e.g.,alpha-N-FMOC-3-(3-pyridyl)-alanine, available from Synthetech, Albany,Oreg.; 1 eq.), N-methylmorpholine (2.5 eq.), and HATU (1.1 eq.), andstirred at room temperature for 4 hr. The mixture is diluted withCH₂Cl₂, washed with 1 M aq. citric acid (2×), water (1×), and 5% aq.NaHCO₃ (2×), dried over Na₂SO₄, and evaporated in vacuo. Compound III isisolated by flash chromatography (CH₂Cl₂→EtOAc).

Step C. Compound III is dissolved in CH₂Cl₂, Pd(PPh₃)₄ (0.07 eq.) andN-methylaniline (2 eq.) are added, and the mixture stirred at roomtemperature for 4 hr. The mixture is diluted with CH₂Cl₂, washed with 1M aq. citric acid (2×) and water (1×), dried over Na₂SO₄, and evaporatedin vacuo. Compound IV is isolated by flash chromatography(CH₂Cl₂→EtOAc+HOAc).

Step D. TentaGel S AC resin (compound V; 1 eq.) is suspended with DMF inthe collection vessel of the ACT357 peptide synthesizer (AdvancedChemTech Inc. (ACT), Louisville, Ky.). Compound IV (3 eq.), HATU (3 eq.)and DIEA (7.5 eq.) in DMF are added and the collection vessel shaken for1 hr. The solvent is removed and the resin washed with NMP (2×), MeOH(2×), and DMF (2×). The coupling of IV to the resin and the wash stepsare repeated, to give compound VI.

Step E. The resin (compound VI) is mixed with 25% piperidine in DMF andshaken for 5 min. The resin is filtered, then mixed with 25% piperidinein DMF and shaken for 10 min. The solvent is removed and the resinwashed with NMP (2×), MeOH (2×), and DMF (2×). The deprotected resin isthen divided equally by the ACT357 from the collection vessel into 16reaction vessels.

Step F. The 16 aliquots of deprotected resin from step E are suspendedin DMF. To each reaction vessel is added the appropriate carboxylic acidVII₁₋₁₆ (R₁₋₁₆CO₂H; 3 eq.), HATU (3 eq.), and DIEA (7.5 eq.) in DMF. Thevessels are shaken for 1 hr. The solvent is removed and the aliquots ofresin washed with NMP (2×), MeOH (2×), and DMF (2×). The coupling ofVII₁₋₁₆ to the aliquots of resin and the wash steps are repeated, togive compounds VII₁₋₁₆.

Step G. The aliquots of resin (compounds VIII₁₋₁₆) are washed withCH₂Cl₂ (3×). To each of the reaction vessels is added 1% TFA in CH₂Cl₂and the vessels shaken for 30 min. The solvent is filtered from thereaction vessels into individual tubes. The aliquots of resin are washedwith CH₂Cl₂ (2×) and MeOH (2×) and the filtrates combined into theindividual tubes. The individual tubes are evaporated in vacuo,providing compounds IX₁₋₁₆.

Step H. Each of the free carboxylic acids IX₁₋₁₆ is dissolved in DMF. Toeach solution is added pyridine (1.05 eq.), followed bypentafluorophenyl trifluoroacetate (1.1 eq.). The mixtures are stirredfor 45 min. at room temperature. The solutions are diluted with EtOAc,washed with 1 M aq. citric acid (3×) and 5% aq. NaHCO₃ (3×), dried overNa₂SO₄, filtered, and evaporated in vacuo, providing compounds X₁₋₁₆.

Example 2 Demonstration of Photolytic Cleavage of T—L—X

A T—L—X compound as prepared in Example 11 was irradiated with near-UVlight for 7 min at room temperature. A Rayonett fluorescence UV lamp(Southern New England Ultraviolet Co., Middletown, Conn.) with anemission peak at 350 nm is used as a source of UV light. The lamp isplaced at a 15-cm distance from the Petri dishes with samples. SDS gelelectrophoresis shows that >85% of the conjugate is cleaved under theseconditions.

Example 3 Preparation of Fluorescent Labeled Primers and Demonstrationof Cleavage of Fluorophore

Synthesis and Purification of Oligonucleotides

The oligonucleotides (ODNs) are prepared on automated DNA synthesizersusing the standard phosphoramidite chemistry supplied by the vendor, orthe H-phosphonate chemistry (Glenn Research Sterling, Va.).Appropriately blocked dA, dG, dC, and T phosphoramidites arecommercially available in these forms, and synthetic nucleosides mayreadily be converted to the appropriate form. The oligonucleotides areprepared using the standard phosphoramidite supplied by the vendor, orthe H-phosphonate chemistry. Oligonucleotides are purified byadaptations of standard methods. Oligonucleotides with 5′-trityl groupsare chromatographed on HPLC using a 12 micrometer, 300 # Rainin(Emeryville, Calif.) Dynamax C-8 4.2×250 mm reverse phase column using agradient of 15% to 55% MeCN in 0.1 N Et₃NH⁺OAc⁻, pH 7.0, over 20 min.When detritylation is performed, the oligonucleotides are furtherpurified by gel exclusion chromatography. Analytical checks for thequality of the oligonucleotides are conducted with a PRP-column(Alitech, Deerfield, Ill.) at alkaline pH and by PAGE.

Preparation of 2,4,6-trichlorotriazine derived oligonucleotides: 10 to1000 μg of 5′-terminal amine linked oligonucleotide are reacted with anexcess recrystallized cyanuric chloride in 10% n-methyl-pyrrolidone inalkaline (pH 8.3 to 8.5 preferably) buffer at 19° C. to 25° C. for 30 to120 minutes. The final reaction conditions consist of 0.15 M sodiumborate at pH 8.3, 2 mg/ml recrystallized cyanuric chloride and 500 ug/mlrespective oligonucleotide. The unreacted cyanuric chloride is removedby size exclusion chromatography on a G-50 Sephadex (Pharmacia,Piscataway, N.J.) column.

The activated purified oligonucleotide is then reacted with a 100-foldmolar excess of cystamine in 0.15 M sodium borate at pH 8.3 for 1 hourat room temperature. The unreacted cystamine is removed by sizeexclusion chromatography on a G-50 Sephadex column. The derived ODNs arethen reacted with amine-reactive fluorochromes. The derived ODNpreparation is divided into 3 portions and each portion is reacted witheither (a) 20-fold molar excess of Texas Red sulfonyl chloride(Molecular Probes, Eugene, Oreg.), with (b) 20-fold molar excess ofLissamine sulfonyl chloride (Molecular Probes, Eugene, Oreg.), (c)20-fold molar excess of fluorescein isothiocyanate. The final reactionconditions consist of 0.15 M sodium borate at pH 8.3 for 1 hour at roomtemperature. The unreacted fluorochromes are removed by size exclusionchromatography on a G-50 Sephadex column.

To cleave the fluorochrome from the oligonucleotide, the ODNs areadjusted to 1×10⁻⁵ molar and then dilutions are made (12, 3-folddilutions) in TE (TE is 0.01 M Tris, pH 7.0, 5 mM EDTA). To 100 μlvolumes of ODNs 25 μl of 0.01 M dithiothreitol (DTT) is added. To anidentical set of controls no DDT is added. The mixture is incubated for15 minutes at room temperature. Fluorescence is measured in a blackmicrotiter plate. The solution is removed from the incubation tubes (150microliters) and placed in a black microtiter plate (DynatekLaboratories, Chantilly, Va.). The plates are then read directly using aFluoroskan II fluorometer (Flow Laboratories, McLean, Va.) using anexcitation wavelength of 495 nm and monitoring emission at 520 nm forfluorescein, using an excitation wavelength of 591 nm and monitoringemission at 612 nm for Texas Red, and using an excitation wavelength of570 nm and monitoring emission at 590 nm for lissamine.

Moles of RFU RFU RFU Fluorochrome non-cleaved cleaved free 1.0 × 10⁵ M6.4 1200 1345 3.3 × 10⁶ M 2.4 451 456 1.1 × 10⁶ M 0.9 135 130 3.7 × 10⁷M 0.3 44 48 1.2 × 10⁷ M 0.12 15.3 16.0 4.1 × 10⁷ M 0.14 4.9 5.1 1.4 ×10⁸ M 0.13 2.5 2.8 4.5 × 10⁹ M 0.12 0.8 0.9

The data indicate that there is about a 200-fold increase in relativefluorescence when the fluorochrome is cleaved from the ODN.

Example 4 Preparation of Tagged M13 Sequence Primers and Demonstrationof Cleavage of Tags

Preparation of 2,4,6-trichlorotriazine derived oligonucleotides: 1000 μgof 5′-terminal amine linked oligonucleotide(5′-hexylamine-TGTAAAACGACGGCCAGT-3″) (Seq. ID No. 1) are reacted withan excess recrystallized cyanuric chloride in 10% n-methyl-pyrrolidonealkaline (pH 8.3 to 8.5 preferably) buffer at 19 to 25 C. for 30 to 120minutes. The final reaction conditions consist of 0.15 M sodium borateat pH 8.3, 2 mg/ml recrystallized cyanuric chloride and 500 ug/mlrespective oligonucleotide. The unreacted cyanuric chloride is removedby size exclusion chromatography on a G-50 Sephadex column.

The activated purified oligonucleotide is then reacted with a 100-foldmolar excess of cystamine in 0.15 M sodium borate at pH 8.3 for 1 hourat room temperature. The unreacted cystamine is removed by sizeexclusion chromatography on a G-50 Sephadex column. The derived ODNs arethen reacted with a variety of am ides. The derived ODN preparation isdivided into 12 portions and each portion is reacted (25 molar excess)with the pentafluorophenyl-esters of either: (1) 4-methoxybenzoic acid,(2) 4-fluorobenzoic acid, (3) toluic acid, (4) benzoic acid, (5)indole-3-acetic acid, (6) 2,6-difluorobenzoic acid, (7) nicotinic acidN-oxide, (8) 2-nitrobenzoic acid, (9) 5-acetylsalicylic acid, (10)4-ethoxybenzoic acid, (11) cinnamic acid, (12) 3-aminonicotinic acid.The reaction is for 2 hours at 37° C. in 0.2 M NaBorate pH 8.3. Thederived ODNs are purified by gel exclusion chromatography on G-50Sephadex.

To cleave the tag from the oligonucleotide, the ODNs are adjusted to1×10⁻⁵ molar and then dilutions are made (12, 3-fold dilutions) in TE(TE is 0.01 M Tris, pH 7.0, 5 mM EDTA) with 50% EtOH (V/V). To 100 μlvolumes of ODNs 25 μl of 0.01 M dithiothreitol (DTT) is added. To anidentical set of controls no DDT is added. Incubation is for 30 minutesat room temperature. NaCl is then added to 0.1 M and 2 volumes of EtOHis added to precipitate the ODNs. The ODNs are removed from solution bycentrifugation at 14,000×G at 4° C. for 15 minutes. The supernatants arereserved, dried to completeness. The pellet is then dissolved in 25 μlMeOH. The pellet is then tested by mass spectrometry for the presence oftags.

The mass spectrometer used in this work is an external ion sourceFourier-transform mass spectrometer (FTMS). Samples prepared for MALDIanalysis are deposited on the tip of a direct probe and inserted intothe ion source. When the sample is irradiated with a laser pulse, ionsare extracted from the source and passed into a long quadrupole ionguide that focuses and transports them to an FTMS analyzer cell locatedinside the bore of a superconducting magnet

The spectra yield the following information. Peaks varying in intensityfrom 25 to 100 relative intensity units at the following molecularweights: (1) 212.1 amu indicating 4-methoxybenzoic acid derivative, (2)200.1 indicating 4-fluorobenzoic acid derivative, (3) 196.1 amuindicating toluic acid derivative, (4) 182.1 amu indicating benzoic acidderivative, (5) 235.2 amu indicating indole-3-acetic acid derivative,(6) 218.1 amu indicating 2,6-difluorobenzoic derivative, (7) 199.1 amuindicating nicotinic acid N-oxide derivative, (8) 227.1 amu indicating2-nitrobenzamide, (9) 179.18 amu indicating 5-acetylsalicylic acidderivative, (10) 226.1 amu indicating 4-ethoxybenzoic acid derivative,(11) 209.1 amu indicating cinnamic acid derivative, (12) 198.1 amuindicating 3-aminonicotinic acid derivative.

The results indicate that the MW-identifiers are cleaved from theprimers and are detectable by mass spectrometry.

Example 5 Preparation of a Set of Compounds of the FormulaR₁₋₃₆-Lys(ε-iNIP)-ANP-Tfp

FIG. 3 illustrates the parallel synthesis of a set of 36 T—L—X compounds(X=L_(h)), where L_(h) is an activated ester (specifically.tetrafluorophenyl ester), L² is an ortho-nitrobenzylamine group with L³being a methylene group that links L_(h) and L², T has a modularstructure wherein the carboxylic acid group of lysine has been joined tothe nitrogen atom of the L² benzylamine group to form an amide bond, anda variable weight component R₁₋₃₆, (where these R groups correspond toT² as defined herein, and may be introduced via any of the specificcarboxylic acids listed herein) is bonded through the α-amino group ofthe lysine, while a mass spec sensitivity enhancer group (introduced viaN-methylisonipecotic acid) is bonded through the ε-amino group of thelysine.

Referring to FIG. 3:

Step A. NovaSyn HMP Resin (available from NovaBiochem; 1 eq.) issuspended with DMF in the collection vessel of the ACT357. Compound I(ANP available from ACT; 3 eq.), HATU (3 eq.) and NMM (7.5 eq.) in DMFare-added and the collection vessel shaken for 1 hr. The solvent isremoved and the resin washed with NMP (2×), MeOH (2×), and DMF (2×). Thecoupling of I to the resin and the wash steps are repeated, to givecompound II.

Step B. The resin (compound II) is mixed with 25% piperidine in DMF andshaken for 5 min. The resin is filtered, then mixed with 25% piperidinein DMF and shaken for 10 min. The solvent is removed, the resin washedwith NMP (2×), MeOH (2×), and DMF (2×), and used directly in step C.

Step C. The deprotected resin from step B is suspended in DMF and to itis added an FMOC-protected amino acid, containing a protected aminefunctionality in its side chain (Fmoc-Lysine(Aloc)-OH, available fromPerSeptive Biosystems; 3 eq.), HATU (3 eq.), and NMM (7.5 eq.) in DMF.The vessel is shaken for 1 hr. The solvent is removed and the resinwashed with NMP (2×), MeOH (2×), and DMF (2×). The coupling ofFmoc-Lys(Aloc)-OH to the resin and the wash steps are repeated, to givecompound IV.

Step D. The resin (compound IV) is washed with CH₂Cl₂ (2×), and thensuspended in a solution of (PPh₃)₄Pd (0) (0.3 eq.) and PhSiH₃ (10 eq.)in CH₂Cl₂. The mixture is shaken for 1 hr. The solvent is removed andthe resin is washed with CH₂Cl₂ (2×). The palladium step is repeated.The solvent is removed and the resin is washed with CH₂Cl₂ (2×),N,N-diisopropylethylammonium diethyldithiocarbamate in DMF (2×), DMF(2×) to give compound V.

Step E. The deprotected resin from step D is coupled withN-methylisonipecotic acid as described in step C to give compound VI.

Step F. The Fmoc protected resin VI is divided equally by the ACT357from the collection vessel into 36 reaction vessels to give compoundsVI₁₋₃₆.

Step G. The resin (compounds VI₁₋₃₆) is treated with piperidine asdescribed in step B to remove the FMOC group.

Step H. The 36 aliquots of deprotected resin from step G are suspendedin DMF. To each reaction vessel is added the appropriate carboxylic acid(R₁₋₃₆CO₂H; 3 eq.), HATU (3 eq.), and NMM (7.5 eq.) in DMF. The vesselsare shaken for 1 hr. The solvent is removed and the aliquots of resinwashed with NMP (2×), MeOH (2×), and DMF (2×). The coupling of R₁₋₃₆CO₂Hto the aliquots of resin and the wash steps are repeated, to givecompounds VII₁₋₃₆.

Step I. The aliquots of resin (compounds VIII₁₋₃₆) are washed withCH₂Cl₂ (3×). To each of the reaction vessels is added 90:5:5TFA:H20:CH₂Cl₂ and the vessels shaken for 120 min. The solvent isfiltered from the reaction vessels into individual tubes. The aliquotsof resin are washed with CH₂Cl₂ (2×) and MeOH (2×) and the filtratescombined into the individual tubes. The individual tubes are evaporatedin vacuo, providing compounds IX₁₋₃₆.

Step J. Each of the free carboxylic acids IX₁₋₃₆ is dissolved in DMF. Toeach solution is added pyridine (1.05 eq.), followed bytetrafluorophenyl trifluoroacetate (1.1 eq.). The mixtures are stirredfor 45 min. at room temperature. The solutions are diluted with EtOAc,washed with 5% aq. NaHCO₃ (3×), dried over Na₂SO₄, filtered, andevaporated in vacuo, providing compounds IX₁₋₃₆.

Example 6 Preparation of a Set of Compounds of the formulaR₁₋₃₆-Lys(ε-iNIP)-NBA-Tfp

FIG. 4 illustrates the parallel synthesis of a set of 36 T—L—X compounds(X=L_(h)), where L_(h) is an activated ester (specifically,tetrafluorophenyl ester), L² is an ortho-nitrobenzylamine group with L³being a direct bond between L_(h) and L², where L_(h) is joined directlyto the aromatic ring of the L² group, T has a modular structure whereinthe carboxylic acid group of lysine has been joined to the nitrogen atomof the L² benzylamine group to form an amide bond, and a variable weightcomponent R₁₋₃₆, (where these R groups correspond to T² as definedherein, and may be introduced via any of the specific carboxylic acidslisted herein) is bonded through the α-amino group of the lysine, whilea mass spec enhancer group (introduced via N-methylisonipecotic acid) isbonded through the ε-amino group of the. lysine.

Referring to FIG. 4

Step A. NovaSyn HMP Resin is coupled with compound I (NBA preparedaccording to the procedure of Brown et al., Molecular Diversity, 1, 4(1995)) according to the procedure described in step A of Example 5, togive compound II.

Steps B-J. The resin (compound II) is treated as described in steps B-Jof Example 5 to give compounds X₁₋₃₆.

Example 7 Preparation of a Set of Compounds of the FormulaiNIP-Lys(ε-R₁₋₃₆)-ANP-Tfp

FIG. 5 illustrates the parallel synthesis of a set of 36 T—L—X compounds(X=L_(h)), where L_(h) is an activated ester (specifically,tetrafluorophenyl ester), L² is an ortho-nitrobenzylamine group with L³being a methylene group that links L_(h) and L², T has a modularstructure wherein the carboxylic acid group of lysine has been joined tothe nitrogen atom of the L² benzylamine group to form an amide bond, anda variable weight component R₁₋₃₆, (where these R groups correspond toT² as defined herein, and may be introduced via any of the specificcarboxylic acids listed herein) is bonded through the α-amino group ofthe lysine, while a mass spec sensitivity enhancer group (introduced viaN-methylisonipecotic acid) is bonded through the α-amino group of thelysine.

Referring to FIG. 5:

Steps A-C. Same as in Example 5.

Step D. The resin (compound IV) is treated with piperidine as describedin step B of Example 5 to remove the FMOC group.

Step E. The deprotected α-amine on the resin in step D is coupled withN-methylisonipecotic acid as described in step C of Example 5 to givecompound V.

Step F. Same as in Example 5.

Step G. The resin (compounds VI₁₋₃₆) are treated with palladium asdescribed in step D of Example 5 to remove the Aloc group.

Steps H-J. The compounds X₁₋₃₆ are prepared in the same manner as inExample 5.

Example 8 Preparation of a Set of Compounds of the FormulaR₁₋₃₆-Glu(γ-DIAEA)-ANP-Tfp

FIG. 6 illustrates the parallel synthesis of a set of 36 T—L—X compounds(X=L_(h)), where L_(h) is an activated ester (specifically,tetrafluorophenyl ester), L² is an ortho-nitrobenzylamine group with L³being a methylene group that links L_(h) and L², T has a modularstructure wherein the α-carboxylic acid group of glutamatic acid hasbeen joined to the nitrogen atom of the L² benzylamine group to form anamide bond, and a variable weight component R₁₋₃₆, (where these R groupscorrespond to T² as defined herein, and may be introduced via any of thespecific carboxylic acids listed herein) is bonded through the aα-aminogroup of the glutamic acid, while a mass spec sensitivity enhancer group(introduced via 2-(diisopropylamino)ethylamine) is bonded through theγ-carboxylic acid of the glutamic acid.

Referring to FIG. 6:

Steps A-B. Same as in Example 5.

Step C. The deprotected resin (compound III) is coupled toFmoc-Glu-(OAl)-OH using the coupling method described in step C ofExample 5 to give compound IV.

Step D. The allyl ester on the resin (compound IV) is washed with CH₂Cl₂(2×) and mixed with a solution of (PPh₃)₄Pd (0) (0.3 eq.) andN-methylaniline (3 eq.) in CH₂Cl₂. The mixture is shaken for 1 hr. Thesolvent is removed and the resin is washed with CH₂Cl₂ (2×). Thepalladium step is repeated. The solvent is removed and the resin iswashed with CH₂Cl₂ (2×), N,N-diisopropylethylammoniumdiethyldithiocarbamate in DMF (2×), DMF (2×) to give compound V.

Step E. The deprotected resin from step D is suspended in DMF andactivated by mixing HATU (3 eq.), and NMM (7.5 eq.). The vessels areshaken for 15 minutes. The solvent is removed and the resin washed withNMP (IX). The resin is mixed with 2-(diisopropylamino)ethylamine (3 eq.)and NMM (7.5 eq.). The vessels are shaken for 1 hour. The coupling of2-(diisopropylamino)ethylamine to the resin and the wash steps arerepeated, to give compound VI.

Steps F-J. Same as in Example 5.

Example 9 Preparation of a Set of Compounds of the FormulaR₁₋₃₆-Lys(ε-iNIP)-ANP-Lys(ε-NH₂)-NH₂

FIG. 7 illustrates the parallel synthesis of a set of 36 T—L—X compounds(X=L_(h)), where L_(h) is an amine (specifically, the ε-amino group of alysine-derived moiety), L² is an ortho-nitrobenzylamine group with L³being a carboxamido-substituted alkyleneaminoacylalkylene group thatlinks L_(h) and L², T has a modular structure wherein the carboxylicacid group of lysine has been joined to the nitrogen atom of the L²benzylamine group to form an amide bond, and a variable weight componentR₁₋₃₆, (where these R groups correspond to T² as defined herein, and maybe introduced via any of the specific carboxylic acids listed herein) isbonded through the α-amino group of the lysine, while a mass specsensitivity enhancer group (introduced via N-methylisonipecotic acid) isbonded through the ε-amino group of the lysine.

Referring to FIG. 7:

Step A. Fmoc-Lys(Boc)-SRAM Resin (available from ACT; compound I) ismixed with 25% piperidine in DMF and shaken for 5 min. The resin isfiltered, then mixed with 25% piperidine in DMF and shaken for 10 min.The solvent is removed, the resin washed with NMP (2×), MeOH (2×), andDMF (2×), and used directly in step B.

Step B. The resin (compound II), ANP (available from ACT; 3 eq.), HATU(3 eq.) and NMM (7.5 eq.) in DMF are added and the collection vesselshaken for 1 hr. The solvent is removed and the resin washed with NMP(2×), MeOH (2×), and DMF (2×). The coupling of I to the resin and thewash steps are repeated, to give compound III.

Steps C-J. The resin (compound III) is treated as in steps B-I inExample 5 to give compounds X₁₋₃₆.

Example 10 Preparation of a Set of Compounds of the FormulaR₁₋₃₆-Lys(ε-Tfa)-Lys(ε-iINP)-ANP-Tfp

FIG. 8 illustrates the parallel synthesis of a set of 36 T—L—X-compounds (X=L_(h)), where L_(h) is an activated ester (specifically,tetrafluorophenyl ester), L² is an ortho-nitrobenzylamine group with L³being a methylene group that links L_(h) and L², T has a modularstructure wherein the carboxylic acid group of a first lysine has beenjoined to the nitrogen atom of the L² benzylamine group to form an amidebond, a mass spec sensitivity enhancer group (introduced viaN-methylisonipecotic acid) is bonded through the ε-amino group of thefirst lysine, a second lysine molecle has been joined to the firstlysine through the α-amino group of the first lysine, a molecular weightadjuster group (having a trifluoroacetyl structure) is bonded throughthe ε-amino group of the second lysine, and a variable weight componentR₁₋₃₆, (where these R groups correspond to T² as defined herein, and maybe introduced via any of the specific carboxylic acids listed herein) isbonded through the α-amino group of the second lysine. Referring to FIG.8:

Steps A-E. These steps are identical to steps A-E in Example 5.

Step F. The resin (compound VI) is treated with piperidine as describedin step B in Example 5 to remove the FMOC group.

Step G. The deprotected resin (compound VII) is coupled toFmoc-Lys(Tfa)-OH using the coupling method described in step C ofExample 5 to give compound VIII.

Steps H-K. The resin (compound VIII) is treated as in steps F-J inExample 5 to give compounds X₁₋₃₆.

Example 11 Preparation of a Set of Compounds of the FormulaR₁₋₃₆-Lys(ε-iNIP)-ANP-5′-AH-ODN

FIG. 9 illustrates the parallel synthesis of a set of 36 T—L—X compounds(X=MOI, where MOI is a nucleic acid fragment, ODN) derived from theesters of Example 5 (the same procedure could be used with other T—L—Xcompounds wherein X is an activated ester). The MOI is conjugated to T—Lthrough the 5′ end of the MOI, via a phosphodiester-alkyleneamine group.

Referring to FIG. 9:

Step A. Compounds XII₁₋₃₆ are prepared according to a modifiedbiotinylation procedure in Van Ness et al., Nucleic Acids Res., 19, 3345(1991). To a solution of one of the 5′-aminohexyl oligonucleotides(compounds XI₁₋₃₆, 1 mg) in 200 mM sodium borate (pH 8.3, 250 mL) isadded one of the Tetrafluorophenyl esters (compounds X₁₋₃₆ from ExampleA, 100-fold molar excess in 250 mL of NMP). The reaction is incubatedovernight at ambient temperature. The unreacted and hydrolyzedtetrafluorophenyl esters are removed from the compounds XII₁₋₃₆ bySephadex G-50 chromatography.

Example 12 Preparation of a Set of Compounds of the FormulaR₁₋₃₆-Lys(ε-iNIP)-ANP-Lys(ε-(MCT-5′-AH-ODN))-NH₂

FIG. 10 illustrates the parallel synthesis of a set of 36 T—L—Xcompounds (X=MOI, where MOI is a nucleic acid fragment, ODN) derivedfrom the amines of Example 11 (the same procedure could be used withother T—L—X compounds wherein X is an amine). The MOI is conjugated toT—L through the 5′ end of the MOI, via a phosphodiester-alkyleneaminegroup.

Referring to FIG. 10:

Step A. The5′-[6-(4,6-dichloro-1,3,5-triazin-2-ylamino)hexyl]oligonucleotidesXII₁₋₃₆ are prepared as described in Van Ness et al., Nucleic AcidsRes., 19, 3345 (1991).

Step B. To a solution of one of the5′-[6-(4,6-dichloro-1,3,5-triazin-2-ylamino)hexyl]oligonucleotides(compounds XII₁₋₃₆) at a concentration of 1 mg/ml in 100 mM sodiumborate (pH 8.3) was added a 100-fold molar excess of a primary amineselected from R₁₋₃₆-Lys(e-iNIP)-ANP-Lys(e-NH₂)-NH₂ (compounds X₁₋₃₆ fromExample 11). The solution is mixed overnight at ambient temperature. Theunreacted amine is removed by ultrafiltration through a 3000 MW cutoffmembrane (Amicon, Beverly, Mass.) using H₂O as the wash solution (3×).The compounds XIII₃₆ are isolated by reduction of the volume to 100 mL.

Example 13 Demonstration of the simultaneous Detection of Multiple Tagsby Mass Spectrometry

This example provides a description of the ability to simultaneouslydetect multiple compounds (tags) by mass spectrometry. In thisparticular example, 31 compounds are mixed with a matrix, deposited anddried on to a solid support and then desorbed with a laser. Theresultant ions are then introduced in a mass spectrometer.

The following compounds (purchased from Aldrich, Milwaukee, Wis.) aremixed together on an equal molar basis to a final concentration of 0.002M (on a per compound) basis: benzamide (121.14), nicotinamide (122.13),pyrazinamide (123.12), 3-amino-4-pyrazolecarboxylic acid (127.10),2-thiophenecarboxamide (127.17), 4-aminobenzamide (135.15), tolumide(135.1.7), 6-methylnicotinamide (136.15), 3-aminonicotinamide (137.14),nicotinamide N-oxide (138.12), 3-hydropicolinamide (138.13),4-fluorobenzamide (139.13), cinnamamide (147.18), 4-methoxybenzamide(151.17), 2,6-difluorbenzamide (157.12),4-amino-5-imidazole-carboxyamide (162.58), 3,4-pyridine-dicarboxyamide(165.16), 4-ethoxybenzamide (165.19), 2,3-pyrazinedicarboxamide(166.14), 2-nitrobenzamide (166.14), 3-fluoro-4-methoxybenzoic acid(170.4), indole-3-acetamide (174.2), 5-acetylsalicylamide (179.18),3,5-dimethoxybenzamide (181.19), 1-naphthaleneacetamide (185.23),8-chloro-3,5-diamino-2-pyrazinecarboxyamide (187.59),4-trifluoromethyl-benzamide (189.00),5-amino-5-phenyl-4-pyrazole-carboxamide (202.22),1-methyl-2-benzyl-malonamate (207.33),4-amino-2,3,5,6-tetrafluorobenzamide (208.11), 2,3-napthlenedicarboxylicacid (212.22). The compounds are placed in DMSO at the concentrationdescribed above. One μl of the material is then mixed withalpha-cyano-4-hydroxy cinnamic acid matrix (after a 1:10,000 dilution)and deposited on to a solid stainless steel support.

The material is then desorbed by a laser using the Protein TOF MassSpectrometer (Bruker, Manning Park, Mass.) and the resulting ions aremeasured in both the linear and reflectron modes of operation. Thefollowing m/z values are observed (FIG. 11):

121.1→benzamide (121.14)

122.1→nicotinamide (122.13)

123.1→pyrazinamide (123.12)

124.1

125.2

127.3→3-amino-4-pyrazolecarboxylic acid (127.10)

127.2→2-thiophenecarboxamide (127.17)

135.1→4-aminobenzamide (135.15)

135.1→tolumide (135.17)

136.2→6-methylnicotinamide (136.15)

137.1→3-aminonicotinamide (137.14)

138.2→nicotinamide N-oxide (138.12)

138.2→3-hydropicolinamide (138.13)

139.2→4-fluorobenzamide (139.13)

140.2

147.3→cinnamamide (147.18)

148.2

149.2

4-methoxybenzamide (151.17)

152.2

2,6-difluorbenzamide (157.12)

158.3

4-amino-5-imidazole-carboxyamide (162.58)

163.3

165.2→3,4-pyridine-dicarboxyamide (165.16)

165.2→4-ethoxybenzamide (165.19)

166.2→2,3-pyrazinedicarboxamide (166.14)

166.2→2-nitrobenzamide (166.14)

3-fluoro-4-methoxybenzoic acid (170.4)

171.1

172.2

173.4

indole-3-acetamide (174.2)

178.3

179.3→5-acetylsalicylamide (179.18)

181.2→3,5-dimethoxybenzamide (181.19)

182.2→

1-naphthaleneacetamide (185.23)

186.2

8-chloro-3,5-diamino-2-pyrazinecarboxyamide (187.59)

188.2

189.2→4-trifluoromethyl-benzamide (189.00)

190.2

191.2

192.3

5-amino-5-phenyl-4-pyrazole-carboxamide (202.22)

203.2

203.4

1-methyl-2-benzyl-malonamate (207.33)

4-amino-2,3,5,6-tetrafluorobenzamide (208.11)

212.2→2,3-napthlenedicarboxylic acid (212.22).

219.3

221.2

228.2

234.2

237.4

241.4

The data indicate that 22 of 31 compounds appeared in the spectrum withthe anticipated mass, 9 of 31 compounds appeared in the spectrum with an+H mass (1 atomic mass unit, amu) over the anticipated mass. The latterphenomenon is probably due to the protonation of an amine within thecompounds. Therefore 31 of 31 compounds are detected by MALDI MassSpectroscopy. More importantly, the example demonstrates that multipletags can be detected simultaneously by a spectroscopic method.

The alpha-cyano matrix alone (FIG. 11) gave peaks at 146.2, 164.1,172.1, 173.1, 189.1, 190.1, 191.1, 192.1, 212.1, 224.1, 228.0, 234.3.Other identified masses in the spectrum are due to contaminants in thepurchased compounds as no effort was made to further purify thecompounds.

Example 14 Microsatellite Markers: PCR Amplifications

The microsatellite markers are amplified utilizing the followingstandard PCR conditions. Briefly, PCR reactions are performed in a totalvolume of 50 μl, containing 40 ng of genomic DNA, 50 pmol of eachprimer, 0.125 mM dNTPs and 1 unit of Taq polymerase. 1×amplificationbuffer contains 10 mM Tris base, pH. 9, 50 mM KCl, 1.5 mM MgCl₂, 0.1%Triton X-100 and 0.01% gelatin. The reactions are performed using a“hot-start” procedure: Taq polymerase is added only after a firstdenaturation step of 5 minutes at 96° C. Amplification is carried outfor 35 cycles: denaturation (94° C. for 40 sec) and annealing (55° C.for 30 sec). An elongation step (72° C. for 2 minutes) ends the processafter the last annealing. Since the amplification products to beobtained are short (90 to 350 base pairs long) and the time interval toraise the temperature from 55° C. to 94° C. (obtained with a rampingrate of 1° C./second) is long enough, completion of DNA elongation canbe achieved without a step at 72° C.

Example 15 Separation of DNA Fragments

Instrumentation

The separation of DNA fragments can be performed using an HPLC systemassembled from several standard components. These components include aminimum of two high pressure pumps which pump solvent through a highpressure gradient mixer, an injector, HPLC column, and a detector. Theinjector is an automated, programmable autosampler capable of storingtypically between eighty and one hundred samples at or below ambienttemperatures to maintain the stability of the sample components. Theautoinjector also is capable of making uL size injections in areproducible manner completely unattended. The HPLC column is containedin a heated column compartment capable of holding a defined temperatureto within 0.1° C. The column used in the examples below was purchasedfrom SeraSep (San Jose, Calif.) under the name DNASep. This column is a55×4.6 mm column with a 2.2 um non-porous polystyrenedivinylbenzenecopolymer particle alkylated with C18. The packing material is stablewithin a pH range of 2-12 and tolerates temperatures as high as 70° C.Detection of analyte was performed using a single or multiple wavelengthUV detector or diode array detector.

Methods

The methods applied in this example for separation of DNA fragments useion-pair chromatography, a form of chromatography in which ions insolution can be paired or neutralized and separated as an ion pair on areversed phase column. The lipophilic character and the concentration ofthe counterion determine the degree of retention of the analyte. In thecase of a DNA molecule the lipophilic, cationic buffer component pairswith anionic phosphate groups of the DNA backbone. The buffer componentsalso interact with the alkyl groups of the stationary phase. The pairedDNA then elutes according to size as the mobile phase is madeprogressively more organic with increasing concentration ofacetonitrile. Evaluation of the suitability of various amine salts wasevaluated using enzymatic digests of plasmids or commercially availableDNA ladders. The range of acetonitrile required to elute the DNA as wellas the temperature of the column compartment varied with each bufferevaluated.

Buffers

The buffers evaluated for their ion-pairing capability were preparedfrom stock solutions. In order to keep the concentration of ion-pairreagent the same throughout the gradient, the ion-pair reagent was addedto both the water and the acetonitrile mobile phases. The column wasequilibrated with a new mobile phase for approximately 18 hours at aflow rate of 50 ul/minute before attempting any separation. Once amobile phase had been evaluated, it was removed and the column cleanedwith a flush of 800 mL 0.1% formic acid in 50% acetonitrile, followed bya flush with 800 mL 0.1% acetic acid in 50% acetonitrile beforeequilibration with a new mobile phase.

A. nn-Dimethyloctylammonium trifluoroacetate

A stock solution of 1 molar dimethyloctylammonium trifluoroacetate wasprepared by mixing one half of an equivalent of trifluoroacetic acid inan appropriate volume of water and slowly adding one equivalent ofnn-Dimethyloctylamine. The pH of this stock solution is 7. The stocksolution was diluted with an appropriate volume of water or acetonitrileto working concentration.

B. nn-Dimethylheptylammonium acetate

A stock solution of 1 molar dimethylheptylammonium acetate was preparedby mixing one equivalent of glacial acetic acid in an appropriate volumeof water and slowly adding one equivalent of nn-Dimethylheptylamine. ThepH of this stock solution is 6.6. The stock solution was diluted with anappropriate amount of water or acetonitrile to working concentration.

C. nn-Dimethylhexylammonium acetate

A stock solution of 1 molar dimethylhexylammonium acetate was preparedby mixing one equivalent of glacial acetic acid in an appropriate volumeof water and slowly adding one equivalent of nn-Dimethylhexylamine. ThepH of this stock solution is 6.5. The stock solution was diluted with anappropriate volume of water or acetonitrile to working concentration.

D. nn-Dimethylbutylammonium acetate

A stock solution of 1 molar dimethylbutylammonium acetate was preparedby mixing one equivalent of glacial acetic acid in an appropriate volumeof water and slowly adding one equivalent of nn-Dimethylbutylamine. ThepH of the stock solution is 6.9. The stock solution was diluted with anappropriate volume of water or acetonitrile to working concentration.

E. nn-Dimethylisopropylammonium acetate

A stock solution of 1 molar dimethylisopropylammonium acetate wasprepared by mixing one equivalent of glacial acetic acid in anappropriate volume of water and slowly adding one equivalent ofnn-Dimethylisopropylamine. The pH of the stock solution is 6.9. Thestock solution was diluted with an appropriate volume of water oracetonitrile to working concentration.

F. nn-Dimethylcyclohexylammonium acetate

A stock solution of 1 molar dimethylcyclohexylammonium acetate wasprepared by mixing one equivalent of glacial acetic acid in appropriatevolume of water and slowly adding one equivalent ofnn-Dimethylcyclohexylamine. The pH of the stock solution is 6.5. Thestock solution was diluted with an appropriate volume of water oracetonitrile to working concentration.

G. Methylpiperidine acetate

A stock solution of 1 molar methylpiperidine acetate was prepared bymixing one equivalent of glacial acetic acid in an appropriate volume ofwater and slowly adding one equivalent of 1-methylpiperidine. The pH ofthe solution is 7. The stock solution was diluted with an appropriatevolume of water or acetonitrile to working concentration.

H. Methylpyrrolidine acetate

A stock solution of 1 molar piperidine acetate was prepared by mixingone equivalent of glacial acetic acid in an appropriate volume of waterand slowly adding one equivalent 1-methylpyrrolidine. The pH of thestock solution is 7. The stock solution was diluted in an appropriatevolume of water or acetonitrile to working concentration.

I. Triethylammonium acetate

A stock solution of 2 molar triethylammonium acetate pH 7.0 waspurchased from Glenn Research Sterling, Va. The stock solution wasdiluted in an appropriate volume of water or acetontrile to workingconcentration.

Example 16 DNA Fingerprint

DNA fingerprinting adaptors are prepared comprising the following: acore sequence and an enzymes specific sequence. The structure of theEcoR1-adapter is 5′-CTCGTAGACTGCGTAC (Seq ID No. 6) the structure of theMse 1-adapter is: 5″-GACGATGAGTCCTGAG (Seq ID No. 7).

Adapters for the rare cutter enzymes were identical to the EcoR1 withthe exception that cohesive ends were used. ALPH primers consists ofthree parts: a core sequence, an enzyme specific sequence and aselective extension sequence. The EcoR1 and Mse1 primers are describedas follows: EcoRI: 5′-gactgcgtaaa-aattc-NNN (Seq ID No. 8); Mse1:5′-gatgagtcctgag-taa-NNN (Seq ID No. 9).

Genomic DNA was incubated for 1 hour at 37° C. with 5 units EcoRI and 5units of MseI in 40 μl volumes with 10 mM Tris-acetate pH 7.5, 10 mMMgAce, 50 mM KAcetate, 5 mM DTT, 50 ng/microliter BSA, 5 mM DTT. Next,10 μl of a solution containing 5 pMol EcoRI adapters, 50 pMol MseIadapters, 1 unit of T4 ligase, 1 mM ATP, in 10 mM Tris-acetate pH 7.5,10 mM MgAce, 50 mM KAcetate, 5 mM DTT, 50 ng/microliter BSA was addedand the incubation was continued for 3 hours at 37° C. Adapters wereprepared by adding equimolar amounts of both strands: adapters were notphosphorylated. After ligation, the reaction mixture was diluted to 500μl with 10 mM Tris HCl, 0.1 mM EDTA pH8.0 and stored at −20° C.

Genetic fingerprinting reactions: Amplification reactions are describedusing DNA templates for the enzyme combination EcoRI/MseI. Genomicfingerprints with other enzyme combinations were performed withappropriate primers. The amplification reactions generally employed twooligonucleotides, one corresponding to the EcoRI pends and onecorresponding to the MseI-ends. One of the two primers was labelled withthe CMST tag, preferably the ECORI primer. The PCR s were performedusing 5 ng labeled EcoRI primer, 30 ng MseI primer, 5 microliters oftemplate DNA, 0.4 units Taq polymerase, 10 mM Tris-HCl, pH 8.3, 1.5 mMMgCL2, 50 mM KCl, 0.2 mM of dATP, dGTP, dCTP, dTTP. The PCR reactionsdiffered depending on the nature of the selective amplificationextensions of the DNA fingerprinting primers used for amplification. DNAfingerprinting reactions with primers having two two or three selectivenucleotides were performed for 36 cycles with the following cycleprofile: a 30 second DNA denaturation step, at 94° C., a 30 secondannealing step at 55° C., and then a 1 minute extension step at 72° C.for 1 minute. The annealing temperature in the first step was 65° C. andwas subsequently reduce for each cycle step by 0.7° C. in the next 12cycles and was continued at 56° C. for the remaining 23 cycles. Allamplifications were performed in a an MJ thermocycler (Watertown Mass.).

DNA fingerprinting of the complex genomes (such as humans) involve twoamplification steps. The preamplification was performed with two DNAfingerprinting having a single selective nucleotide as described abovewith the exception that 30 ng of both DNA fingerprinting primers wasused and that these primers were not labelled with CMST, after thepreamplification step, the reaction mixtures were diluted 10-fold withwith 10 mM Tris-HCl, 0.1 mM EDTA, pH 8.0, and used as templates for thesecond amplification reaction. The second amplification reaction wasperformed as described above for DNA fingerprinting reactions withprimers having the longer selective extensions.

The products from the amplification reactions were analyzed by HPLC.HPLC was carried out using automated HPLC instrumentation (Rainin,Emeryville, Calif., or, Hewlett Packard, Palo Alto, Calif.). UnpurifiedDNA fingerprinting products which had been denatured for 3 minutes at 95prior into injection into an HPLC were eluted with linear acetonitrile(ACN, J. T. Baker, N.J.) gradient of 1.8%/minute at a flow rate of 0.9ml/minute, The start and end points were adjusted according to the sizeof the amplified products. The temperature required for the successfulresolution of the molecules generated during the DNA fingerprintingtechnique was 50° C. The effluent from the HPLC was then directed into amass spectrometer (Hewlett Packard, Palo Alto, Calif.) for the detectionof tags.

The following fragments eluted in the order presented (The number sitedare the positions within the lambda genome at which a cleavage siteoccurred): 47, 78, 91, 733, 1456, 2176, 3275, 3419, 4349, 444, 5268,5709, 6076, 6184, 6551, 7024, 7949, 8062, 8200, 8461, 9079, 9253, 9692,9952, 11083, 11116, 11518, 11584, 12619, 12967, 14108, 14892, 15628,15968, 16034, 16295, 16859, 18869, 19137, 19482, 20800, 21226, 21441,2635, 21702, 21903, 21948, 22724, 23048, 23084, 23111, 23206, 23279,23285, 23479, 23498, 23555, 23693, 23887, 23979, 23987, 24073, 24102,24751, 24987, 25170, 25255, 25353, 25437, 26104, 25578, 25746, 25968,26133, 26426, 26451, 26483, 26523, 26585, 26651, 26666, 26679, 26693,26763, 26810, 26984, 26993, 27038, 27092, 27203, 27317, 27683, 28456,28569, 28922, 28972, 29374, 29981, 30822, 30620, 30639, 30722, 30735,30756, 31169, 31747, 31808, 32194, 32218, 32641, 32704, 33222, 33351,33688, 33736, 33748, 33801, 34202, 34366, 34406, 34590, 34618, 34684,34735, 34753, 34831, 35062, 35269, 35534, 35541, 36275, 36282, 36303,36430, 36492, 36531, 36543, 36604, 36736, 36757, 36879, 37032, 37442,37766, 37783, 37882, 37916, 37994, 36164, 38287, 38412, 38834, 39168,44972, 39607, 39835, 40127, 40506, 40560, 40881, 41017, 41423, 41652,41715, 42317, 42631, 42651, 42673, 42814,. 43410, 43492, 43507, 43528,43593, 44424, 44538, 44596, 44868, 45151, 45788, 46033, 46408, 46556,46804, 46843, 46853, 46896, 46952, 47256, 47274, 47287, 47430, 47576,47699, 47799, 48059, 48125, 48227, 48359, 48378. The average fragmentlength was about 160 nt. The observed sites of cleavage were largely(>95%) compatible with that predicted from an MSE1/RcoR1 digest map.

Example 17 Single Nucleotide Extension Assays

RNA preparation: Total RNA was isolated was prepared from Jurkat cellsusing (starting with 1×10⁹ cells in exponential growth) using an RNAisolation kit from Promega (WI). RNA was stored in two aliquots: 1)stock aliquote in diethyl pyrocarbonate-treated ddH2O was stored at −20°C., and 2) long term storage as a suspension in 100% H₂O.

Reverse Transcription: Poly(dT) primed reverse transcription of totalRNA was performed as described as described in Ausubel et al. (Ausubelet al., in Current Protocols in Molecular Biology, 1991, GreenePublishing Associates/Wiley-Interscience, NY, N.Y.) except that thereaction(s) were scaled to using 1 μg input total RNA. 20-50 units ofreverse transcriptase (Promega) was diluted 10-fold in 10% glycerol, 10mM KPO4 pH 7.4, 0.2% Triton X-100, and 2 mM DTT and placed on ice for 30minutes prior to addition to the reactions. Gene-specific reversetranscription for GADPH and other control genes as described in thefigures and tables were performed using 1 μg of total Jurkat RNAreversed transcribed in 10 mM Tris-HCl pH 8.3, 50 mM KCl, M MgCL2, 1 mMdNTPs, 2 U/μl RNAsin (Gibco-BRL), 0.1 μM oligomer and 0.125 U/μl ofM-MLV reverse transcriptase (Gibco-BRL) in 20 μl reactions. Reactionswere incubated in at 42° C. for 15 minutes, heat inactivated at 95° C.for 5 minutes , and diluted to 100 μl with a master mix of (10 mM TrisHCl pH 8.3, 1 mM NH4Cl, 1.5 M MgCl2, 100 mM KCl), 0.125 mM NTPs, 10ng/ml of the respective oligonucleotide primers and 0.75 units of TAQpolymerase (Gibco-BRL) in preparation for PCR amplification.

PCR: PCR for each gene was performed with gene specific primers spanninga known intron/exon boundry (see tables below). All PCRs were done in 20μl volumes containing 10 mM Tris HCl pH 8.3, 1 mM NH4Cl, 1.5 M MgCl2,100 mM KCl), 0.125 mM NTPs, 10 ng/ml of the respective oligonucleotideprimers and 0.75 units of TAQ polymerase (Gibco-BRL). Cycling parameterswere 94° C. preheating step for 5 minutes followed by 94° C. denaturingstep for 1 minute, 55° C. annealing step for 2 minutes, and a 72° C.extension step for 30 seconds to 1 minute and a final extension at 72°C. for 10 minutes. Amplifications were generally 30-45 in number.

Purification of templates: PCR products were gel purified as describedby Zhen and Swank (Zhen and Swank, BioTechniques, 14(6):894-898, 1993).PCR products were resolved on 1% agarose gels run in 0.04 MTris-acetate, 0.001 M EDTA (1×TEA) buffer and stained with ethidiumbromide while visualizing with a UV light source. A trough was cut justin front of the band of interest and filled with 50-200 μl of 10% PEG in1×TAE buffer. Electrophoresis was continued until the band hadcompletely entered the trough. The contents was then removed andextracted with phenol, cholorform extracted, and then precipitated in0.1 volume of 7.5 M ammonium acetate and 2.5 volumes of 100% EtOH.Samples were washed with 75% EtOH and briefly dried at ambienttemperature. Quantitation of yield was done by electrophoresis of asmall aliquot on 1% agarose gel in 1×TBE buffer with ethidium bromidestaining and comparison to a known standard.

Each SNuPE reaction was carried out in a 50 μl volume containing about100 ng of the amplified DNA fragment, 1 μM of the SNuPE primer, 2 unitsof Tag polymerase, and 1 ul of the appropriate dNTP. All dNTPs areunlabelled in this type of assay. The buffer used was 10 mM Tris-HCl (pH8.3), with 50 mM KCl, 5mM MgCl2 and 0.001% (wt/vol) gelatin. The sampleswere subjected to one cycle consisting of a 2-minute denaturation periodat 95° C., a 2 minute annealing period at 60° C. and a 2-minute primerextension period at 72° C. The sequence of the SNUPE primer for eachfamily is described below.

Primer extensions: Single nucleotide primer extensions were performed asdescribed in Singer-Sam et al., (Singer-Sam et al., PCR Methods andApplications 1:160-163, 1992) except that 1 mM Mg++, 0.1 μM primer, and0.05 μM of each dNTP type was used in each reaction type. After eachprimer extension described above, one-fifth volume of a loading dye (80%formamide, 0.1% bromophenol blue, 0.1% xylene cyanol, 2 mM EDTA) wasadded, and the entire sample electrophoresed in 15% denaturingpolyacrylamide gel. Gels were fixed in 10% glycerol, 10% methanol, 10%glacial acetic acid with constant shaking followed by washing steps with10% glycerol. The gels were then dried at 55° C. for 3-5 hours.

The primers described in this experiment are described by Rychlik(Rychlik, BioTechniques 18:84-90, 1995) Primers may be synthesized orobtained as gel-flirtation grade primers from Midland Certified ReagentCompany (Midland Tex.). The amplifications are either TAQ DNApolymerase-based (10 mM Tris-HCl pH 8.3, 1.5 mM MgCl2, 50 mM KCl) or PfuDNA polymerase-based based (20 mM Tris-HCl pH 8.3, 2.0 mM MgCl2, 10 mMKCl, 10 mM (NH4)2SO4, 0.1% Triton X-100, 0.1 mg/ml bovine serumalbumin). The total nucleoside triphosphate (NTPs) concentration in thereactions is 0.8 mM, the primer concentration is 200 nM (unlessotherwise stated) and the template amount is 0.25 ng of bacteriophagelambda DNA per 20 μl reaction. Cycling parameters were 94° C. preheatingstep for 5 minutes followed by 94° C. denaturing step for 1 minute, 55°C. annealing step for 2 minutes, and a 72° C. extension step for 30seconds to 1 minute and a final extension at 72° C. for 10 minutes.Amplifications were generally 30-45 in number.

Two regions in the bacteriophage lambda genome (GenBank Accession#J02459) were chosen as the priming sites for amplification. The5′-primer has a stable GC-rich 3′-end: the 3′ primer is chosen so that a381 bp product will result. The 5′ forward primer is H17:5′-GAACGAAAACCCCCCGC (Seq ID No. 10). The 3′-reverse primer is RP 17:5′-GATCGCCCCCAAAA (Seq ID No. 11).

The amplified product was then tested for the presence of a polymorphismat position 31245. The following primer was used in four, singlenucleotide extension assays; SNE17: 5′-GAACGAAAACCCCCGC (Seq ID No. 12).The four single nucleotide extension assays were then carried asdescribed above. All the reactions are then pooled and 5 μl of thepooled material was injected onto the HPLC column (SeraSep, San Jose,Calif.) without further purification.

HPLC was carried out using automated HPLC instrumentation (Rainin,Emeryville, Calif., or, Hewlett Packard, Palo Alto, Calif.). UnpurifiedSNEA products which had been denatured for 3 minutes at 95 prior intoinjection into an HPLC were eluted with linear acetonitrile (ACN, J. T.Baker, N.J.) gradient of 1.8%/minute at a flow rate of 0.9 ml/minute,The start and end points were adjusted according to the size of the SNEAproduct. The temperature required for the successful resolution of theSNEA molecules was 50° C. The effluent from the HPLC was then directedinto a mass spectrometer (Hewlett Packard, Palo Alto, Calif.) for thedetection of tags.

Results: Tagged Primer ddNTP type retention time extended? SNE17-487ddATP 2.5 minutes no SNE17-496 ddGTP 2.5 minutes no SNE17-503 ddCTP 4.6minutes yes SNE17-555 ddTTP 2.5 minutes no

The results therefore indicate that the mass spectrometer tag (CMST) tagwas detected at a retention time of 4.6 minutes indicating that theSNE17 primer was extended by one base (ddCTP) and therefore thepolymorphism was position 31245 was in this case a “G”. The SNE17-487,SNE17-496, and SNE17-555 tagged primers were not extended and theirretention times on the HPLC was 2.5 minutes respectively.

Example 18

In this Example (18), all reactions were conducted in foil-coveredflasks. The sequence of reactions A→F described in this Example isillustrated in FIGS. 19A and 19B. Compound numbers as set forth in thisExample refer to the compounds of the same number in FIGS. 19A and 19B.

A. To a solution of ANP linker (compound 1, 11.2 mmol) anddiisopropylethylamine (22.4 mmol) in CHCl₃ (60 mi) was added allylbromide (22.4 mmol). The reaction mixture was refluxed for 3 hours,stirred at room temperature for 18 hours, diluted with CHCl₃ (200 ml),and washed with 1.0 M HCl (2×150 ml) and H₂O (2×150 ml). The organicextracts were dried (MgSO₄) and the solvent evaporated to give compound2 as a yellow solid.

To a mixture of compound 2 in CH₂Cl₂ (70 ml), tris (2-aminoethyl) amine(50 ml) was added and the reaction mixture stirred at room temperaturefor 18 hours. The reaction was diluted with CH₂Cl₂ (150 ml) and washedwith pH 6.0 phosphate buffer (2×150 ml). The organic extracts were dried(MgSO₄) and the solvent evaporated. The residue was subjected to columnchromatography (hexane/EtOAc) to give 1.63 g (58%) of compound 3: ¹H NMR(DMSO-d₆): δ 7.85 (dd, 2H), 7.70 (t, 1H), 7.43 (t, 1H), 5.85 (m, 1H),5.20 (q, 2H), 4.58 (q, 1H), 4.50 (d, 2H), 2.70 (m, 2H), 2.20 (br s, 2H).

B. To a solution of Boc-5-aminopentanoic acid (1.09 mmol) and NMM (3.27mmol) in dry DMF (6 ml), was added HATU (1.14 mmol) and the reactionmixture stirred at room temperature for 0.5 hours. A solution ofcompound 3 (1.20 mmol) in dry DMF (1 ml) was added and the reactionmixture stirred at room temperature for 18 hours. The reaction wasdiluted with EtOAc (50 ml) and washed with 1.0 M HCl (2×50 ml) and D.I.H₂O (2×50 ml). The organic extracts were dried (MgSO₄) and evaporated todryness. The residue was subjected to column chromatography to give 420mg (91%) of compound 4: ¹H NMR (DMSO-d₆): δ 8.65 (d, 1H), 7.88 (d, 1H),7.65 (m, 2H), 7.48 (t, 1H), 6.73 (br s, 1H), 5.85 (m, 1H), 5.55 (m, 1H),5.23 (q, 2H), 4.55 (d, 2H), 2.80 (m, 2H), 2.05 (t, 2H), 1.33 (s, 9H),1.20-1.30 (m, 4H).

C. A solution of compound 4 (0.9 mmol) in HCl.1,4-dioxane (20 mmol) wasstirred at room temperature for 2 hours. The reaction mixture wasconcentrated, dissolved in MeOH and toluene, and concentrated again (5×5ml) to give 398 mg (quantitative) of the compound 5: ¹H NMR (DMSO-d₆): δ8.75 (d, 1H), 7.88 (d, 1H), 7.65 (m, 2H),7.51 (t, 1H), 7.22 (m, 2H),5.85(m, 1H), 5.57 (m, 1H), 5.23 (q, 2H), 4.55 (d, 2H), 2.80 (m, 2H), 2.71(m, 2H), 2.07 (s, 2H), 1.40-1.48 (br s, 4H)

D. To a solution of compound 21 (0.48 mmol, prepared according toExample 20) and NMM (1.44 mmol) in dry DMF (3 ml), was added HATU (0.50mmol) and the reaction mixture stirred at room temperature for 0.5hours. A solution of compound 5 (0.51 mmol) in dry DMF (3 ml) was addedand the reaction stirred at room temperature for 18 hours. The reactionmixture was diluted with EtOAc (75 ml) and washed with 5% Na₂CO₃ (3×50ml). The organic extracts were dried (MgSO₄) and the solvent evaporatedto give 281 mg (78%) of compound 6: ¹H NMR (DMSO-d₆): δ 8.65 (d, 1H),8.17 (d, 1H), 7.82-7.95 (m, 4H), 7.68 (m, 3H), 7.50 (t, 1H), 6.92 (d,1H), 5.85 (m, 1H), 5.57 (m, 1H), 5.20 (q, 2H), 4.55 (d, 2H), 4.30 (q,1H), 4.05 (q, 2H), 2.95 (m, 4H), 2.80 (m, 2H), 2.72 (m, 2H), 2.05 (s,3H), 2.01 (t, 2H), 1.58-1.77 (m, 3H), 1.0 (m, 4H), 1.30 (q, 3H),1.17-1.40 (m, 9H).

E. To a mixture of compound 6 (0.36 mmol) in THF (4 ml), was added 1 MNaOH (1 mmol) and the reaction stirred at room temperature for 2 hours.The reaction mixture was acidified to pH 7.0 with 1.0 M HCl (1 ml) andthe solvent evaporated to give compound 7 (quantitative): ¹H NMR(DMSO-d₆): δ 8.65 (d, 1H), 8.17 (d, 1H), 7.82-7.95 (m, 4H), 7.68 (m,3H), 7.50 (t, 1H), 6.92 (d, 1H), 5.52 (m, 1H), 4.30 (q, 1H), 4.05 (q,2H), 2.95 (m, 4H), 2.80 (m, 2H), 2.72 (m, 2H), 2.05 (s, 3H), 2.01 (t,2H), 1.58-1.77 (m, 3H), 1.50 (m, 4H), 1.30 (q, 3H), 1.17-1.40 (m, 9H).

F. To a solution of compound 7 (0.04 mmol) and NMM (0.12 mmol) in dryDMF (0.4 ml), was added HATU (0.044 mmol) and the reaction stirred atroom temperature for 0.5 hours. Allylamine (0.12 mmol) was added and thereaction mixture stirred at room temperature for 5 hours. The reactionmixture was diluted with EtOAc (15 ml) and washed with 5% Na₂CO₃ (3×10ml). The organic extracts were dried (MgSO₄) and the solvent evaporatedto yield 15 mg (49%) of compound 8: ¹H NMR (DMSO-d₆) δ 8.49 (d, 1H),8.17 (d, 1H), 7.82-7.95 (m, 4H), 7.68 (m, 3H), 7.50 (t, 1H), 6.92 (d,1H), 5.72 (m, 1H), 5.50 (m, 1H), 5.03 (q, 2H), 4.37 (d, 2H), 4.30 (q,1H), 4.05 (q, 2H), 2.95 (m, 4H), 2.80 (m, 2H), 2.72 (m, 2H), 2.05 (s,3H), 2.01 (t, 2H), 1.58-1.77 (m, 3H), 1.50 (m, 4H), 1.30 (q, 3H),1.17-1.40 (m, 9H).

Example 19

The sequence of reactions A→G as described in this Example 19 isillustrated in FIGS. 20A and 20B. Compound numbers as set forth in thisExample refer to the compounds of the same number in FIGS. 20A and 20B.

A. To a solution of Fmoc-Lys(Boc)-OH (compound 9, 33.8 mmol) in CHCl₃(200 ml), was added diisopropylethylamine (67.5 mmol) and allyl bromide(67.5 mmol). The reaction mixture was refluxed for 6 hours, stirred atroom temperature for 16 hours, diluted with CHCl₃, washed with 1.0 M HCl(2×150 ml), saturated NaHCO₃ (1×150 ml) and D.I. H₂O (2×150 ml). Theorganic extracts were dried (MgSO₄) and the solvent evaporated to yieldcompound 10.

To a solution of compound 10 in CHCl₃ (90 ml), was added pyrrolidine (10eq.) and the reaction was stirred at room temperature for 2.5 hours. Thereaction mixture was diluted with CHCl₃ (150 ml) and washed withsaturated NaHCO₃ (3×250 ml). The organic extracts were dried (MgSO₄) andthe solvent evaporated. The residue was subjected to columnchromatography (EtOAc/MeOH) to give 6.52 g (67%) of compound 11: ¹H NMR(CDCl₃): δ 5.90 (m, 1H), 5.27 (m, 2H), 4.60 (d, 2H), 3.48 (t, 1H), 3.10(d, 2H), 1.40-1.78 (m, 9H),1.40 (s, 9H).

B. To a solution of N-methylisonipecotic acid (1.60 mmol) and N-methylmorpholine (4.80 mmol) in dry DMF (5 ml), was added HATU (1.67 mmol).After 0.5 hours, a solution of compound 11 (1.75 mmol) in dry DMF (2 ml)was added and the reaction mixture stirred at room temperature for 18hours. The reaction mixture was diluted with CH₂CL₂ (60 ml) and washedwith saturated Na₂CO₃ (3×40 ml). The organic extracts were dried (MgSO₄)and the solvent evaporated. The residue was subjected to columnchromatography (CH₂Cl₂/MeOH/triethylamine) to give 580 mg (88%) ofcompound 12: ¹H NMR (DMSO): δ 8.12 (d, 1H), 6.77 (t, 1H), 5.90 (m, 1H),5.27 (m, 2H), 4.53 (d, 2H), 4.18 (m, 1H),2.62-2.90 (m, 5H), 2.13 (s,3H),1.85 (m, 2H),1.57 (m, 5H),1.35 (s, 9H), 1.00 (t, 2H).

C. A mixture of compound 12 (1.39 mmol) in HCl.1,4-dioxane (20 mmol) wasstirred at room temperature for 4 hours. The reaction mixture wasconcentrated, dissolved in MeOH, coevaporated with toluene (5×5ml) togive 527 mg (quantitative) of compound 13: ¹H NMR (DMSO-d₆): δ 8.12 (d,1H), 6.77 (t, 1H), 5.90 (m, 1H), 5.27 (m, 2H), 4.53 (d, 2H), 4.18 (m,1H),2.65-3.00 (m, 8H), 2.23 (s, 3H),1.85 (m, 2H),1.57 (m, 5H), 1.00 (t,2H).

D. To a solution of 4-ethoxybenzoic acid (1 eq.) in dry DMF, is addedNMM (3 eq.) and HATU (1.05 eq.). After 0.5 hours, a solution of compound13 in dry DMF is added. After the completion of the reaction and basicworkup, the compound 14 is isolated and purified.

E. To a solution of compound 14 in THF, is added 1N NaOH and thereaction mixture stirred at room temperature. After the completion ofthe reaction and acidification, the compound 15 is isolated.

F. To a solution of compound 15 (1 eq.) in dry DMF, is added NMM (3 eq.)and HATU (1.05 eq.). After 0.5 hours, a solution of compound 21(ANP—allyl ester, prepared according to Example 20) in dry DMF is added.After the completion of the reaction and basic workup, the titlecompound 16 is isolated and purified.

G. To a solution of compound 16 in THF, is added 1N NaOH and thereaction mixture stirred at room temperature. After the completion ofthe reaction and acidification, the compound 17 is isolated.

Example 20

The sequence of reaction A through D as described in this Example 20 isillustrated in FIG. 21. Compound numbers as set forth in this Example,as well as Examples 18 and 19, refer to the compounds of the same numberin FIG. 21.

A. To a solution of 4-ethoxybenzoic acid (7.82 mmol) and N-methylmorpholine (20.4 mmol) in CH₂Cl₂ (10 ml), was added HATU (7.14 mmol).After 0.25 hours, a solution of compound 11 (6.8 mmol) in CH₂Cl₂ (6 ml)was added and the reaction mixture stirred at room temperature for 18hours. The reaction was diluted with CH₂Cl₂ (150 ml) and washed with 1.0M HCl (3×50 ml) and saturated NaHCO₃ (3×50 ml). The organic extractswere dried (MgSO₄) and the solvent evaporated. The residue was subjectedto column chromatography (CH₂Cl₂/MeOH) to give 2.42 g (82%) of compound18: ¹H NMR (CDCl₃): δ 7.78 (d, 2H), 6.91 (d, 2H), 6.88 (d, 1H),5.83-5.98 (m, 1H), 5.21-5.38 (m, 2H), 4.80 (q, 1H), 4.66 (d, 2H), 4.06(q, 2H), 3.11 (q, 2H), 1.90-2.04 (m, 1H), 1.68-1.87 (m, 1H), 1.39 (t,3H), 1.34 (s, 9H), 1.32-1.58 (m, 4H).

B. A mixture of compound 18 (5.5 mmol) in HCl.1,4-dioxane (14.3 mmol)was stirred at room temperature for 1 hour. The reaction mixture wasconcentrated, dissolved in MeOH, azeotroped with toluene, andconcentrated again (5×5 ml) to give a quantitative yield of compound 19.

C. To a solution of N-methylisonipecotic acid (6.21 mmol) in dry DMF (15mL), was added NMM (21.6 mmol) and HATU (5.67 mmol). After 0.5 hours, asolution of compound 19 (5.4 mmol) in dry DMF (10 ml) was added and thereaction stirred at room temperature for 18 hours. The reaction mixturewas brought to pH 12 with 1N NaOH (20 ml) and extracted with CHCl₃(2×200 ml). The organic extracts were dried (MgSO₄) and the solventevaporated to give 2.2 g (89%) of compound 20: ¹H NMR (DMSO-d₆): δ 8.52(d, 1H), 7.84 (d, 2H), 7.72 (t, 1H), 6.95 (d, 2H), 5.80-5.95 (m, 1H),5.18-5.31 (dd, 2H), 4.58 (d, 2H), 4.37 (q, 1H), 4.08 (q, 2H), 3.01 (d,2H), 2.08 (s, 3H), 1.95 (m, 1H), 1.63-1.82 (m, 4H), 1.51 (m, 4H), 1.32(t, 3H), 1.22-1.41 (m, 6H).

D. To a solution of compound 20 (4.4 mmol) in THF (10 ml), is added 1NNaOH (4.4 mmol) and the reaction mixture stirred at room temperature for1 hour. The reaction was concentrated, dissolved in THF/toluene (2×5ml), concentrated, dissolved in CH₂Cl₂/toluene (1×5 ml) and concentratedagain to give a quantitative yield of compound 21: ¹H NMR (DMSO-d₆): δ7.76 (d, 2H), 6.96 (d, 2H), 4.04 (q, 2H), 3.97 (d, 1H), 2.97 (d, 2H),2.64 (d, 2H), 2.08 (s, 3H), 1.95 (m, 1H), 1.58-1.79 (m, 4H), 1.44 (m,6H), 1.30 (t, 3H), 1.11-1.35 (m, 4H).

From the foregoing, it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention.

11 18 base pairs nucleic acid single linear 1 TGTAAAACGA CGGCCAGT 18 13base pairs nucleic acid single linear 2 AAGCTTCGAC TGT 13 13 base pairsnucleic acid single linear 3 AAGCTTTGGT CAG 13 13 base pairs nucleicacid single linear 4 AAGCTTCTCA ACG 13 13 base pairs nucleic acid singlelinear 5 AAGCTTAGTA GGC 13 17 base pairs nucleic acid single linear 6CTCGTAGACT GCGTACC 17 16 base pairs nucleic acid single linear 7GACGATGAGT CCTGAG 16 19 base pairs nucleic acid single linear 8GACTGCGTAA AAATTCNNN 19 19 base pairs nucleic acid single linear 9GATGAGTCCT GAGTAANNN 19 17 base pairs nucleic acid single linear 10GAACGAAAAC CCCCCGC 17 20 base pairs nucleic acid single linear 11GATCGCCCCC AAAACACATA 20

We claim:
 1. A method for determining the identity of a nucleic acidmolecule, comprising sequentially: (a) generating tagged nucleic acidmolecules from one or more selected target nucleic acid molecules,wherein a tag is correlative with a particular nucleic acid fragment anddetectable by non-fluorescent spectrometry or potentiometry; (b)separating said tagged molecules by size; (c) cleaving said tag fromsaid tagged molecule; and (d) detecting said tag by non-fluorescentspectrometry or potentiometry, and therefrom determining the identity ofsaid nucleic acid molecule.
 2. A method for detecting a selected nucleicacid molecule, comprising sequentially: (a) combining a tagged nucleicacid probe with target nucleic acid molecules under conditions and for atime sufficient to permit hybridization of said tagged nucleic acidprobe to a complementary selected target nucleic acid sequence, whereinsaid tagged nucleic acid probe is detectable by non-fluorescentspectrometry or potentiometry; (b) increasing or decreasing the size ofsaid hybridized tagged probes, the size of unhybridized probes or targetmolecules, or the size of the probe:target hybrids; (c) separating thetagged probes by size; (d) cleaving said tag from said tagged probe; and(e) detecting said tag by non-fluorescent spectrometry or potentiometry,and therefrom detecting said selected nucleic acid molecule.
 3. Themethod according to claims 1 or 2 wherein the detection of the tag is bymass spectrometry, infrared spectrometry, ultraviolet spectrometry, or,potentiostatic amperometry.
 4. The method according to claim 1 whereingreater than 4 tagged nucleic acid fragments are generated and whereineach tag is unique for a selected nucleic acid fragment.
 5. The methodaccording to claim 2 wherein greater than 4 tagged nucleic acid probesare utilized and wherein each tag is unique for a selected nucleic acidprobe.
 6. The method according to claims 1 or 2 wherein said targetnucleic acid molecule is generated by primer extension.
 7. The methodaccording to claim 2 wherein the size of said hybridized tagged probes,unhybridized probes or target molecules, or probe:target hybrids arealtered by a method selected from the group consisting of polymeraseextension, ligation, exonuclease digestion and endonuclease digestion.8. The method according to claims 1 or 2 wherein said tagged moleculesare separated by a method selected from the group consisting of gelelectrophoresis, capillary electrophoresis, micro-channelelectrophoresis, HPLC, size exclusion chromatography and filtration. 9.The method according to claims 1 or 2 wherein said tagged molecules arecleaved by a method selected from the group consisting of oxidation,reduction, acid-labile, base labile, enzymatic, electrochemical, thermaland photolabile methods.
 10. The method according to claim 1 or 2wherein said tag is detected by a method selected from a groupconsisting of time-of-flight mass spectrometry, quadrupole massspectrometry, magnetic sector mass spectrometry and electric sector massspectrometry.
 11. The method according to claim 10 wherein said tag isdetected by potentiostatic amperometry utilizing detectors selected fromthe group consisting of coulometric detectors and amperometricdetectors.
 12. The method according to claims 1 or 2 wherein the stepsof separating, cleaving and detecting are performed in a continuousmanner.
 13. The method according to claims 1 or 2 wherein the stepsseparating, cleaving and detecting are performed in a continuous manneron a single device.
 14. The method according to claim 13 wherein thesteps of separating, cleaving and detecting are automated.
 15. Themethod according to claims 1 or 2 wherein said tagged molecules orprobes are generated from 5′-tagged oligonucleotide primers.
 16. Themethod according to claims 1 or 2 wherein said tagged molecules orprobes are generated from tagged dideoxynucleotide terminators.
 17. Amethod for genotyping a selected organism, comprising sequentially: (a)generating tagged nucleic acid molecules from a selected targetmolecule, wherein a tag is correlative with a particular fragment andmay be detected by non-fluorescent spectrometry or potentiometry; (b)separating said tagged molecules by sequential length; (c) cleaving saidtag from said tagged molecule; and (d) detecting said tag bynon-fluorescent spectrometry or potentiometry, and therefrom determiningthe genotype of said organism.
 18. A method for genotyping a selectedorganism, comprising sequentially: (a) combining a tagged nucleic acidmolecule with a selected target molecule under conditions and for a timesufficient to permit hybridization of said tagged molecule to saidtarget molecule, wherein a tag is correlative with a particular fragmentand may be detected by non-fluorescent spectrometry or potentiometry;(b) separating said tagged molecules by sequential length; (c) cleavingsaid tag from said tagged molecule; and (d) detecting said tag bynon-fluorescent spectrometry or potentiometry, and therefrom determiningthe genotype of said organism.
 19. The method according to claims 17 or18 wherein said tagged molecules are generated from a pool of clonesselected from the group consisting of genomic clones, cDNA clones andRNA clones.
 20. The method according to claims 17 or 18 wherein saidtagged molecules are generated by polymerase chain reaction.
 21. Themethod according to claims 17 or 18 wherein the detection of the tag isby mass spectrometry, infrared spectrometry, ultraviolet spectrometry,or, potentiostatic amperometry.
 22. The method according to claims 17 or18 wherein greater than 4 tagged nucleic acid molecules are generatedand wherein each tag is unique for a selected nucleic acid fragment. 23.The method according to claims 17 or 18 wherein said target nucleic acidmolecule is generated by primer extension.
 24. The method according toclaims 17 or 18 wherein said tagged molecules are separated by a methodselected from the group consisting of gel electrophoresis, capillaryelectrophoresis, micro-channel electrophoresis, HPLC, size exclusionchromatography and filtration.
 25. The method according to claims 17 or18 wherein said tagged molecules are cleaved by a method selected fromthe group consisting of oxidation, reduction, acid-labile, base labile,enzymatic electrochemical, thermal and photolabile methods.
 26. Themethod according to claims 17 or 18 wherein said tag is detected bytime-of-flight mass spectrometry, quadrupole mass spectrometry, magneticsector mass spectrometry and electric sector mass spectrometry.
 27. Themethod according to claims 17 or 18 wherein said tag is detected bypotentiostatic amperometry utilizing detectors selected from the groupconsisting of coulometric detectors and amperometric detectors.
 28. Themethod according to claims 17 or 18 wherein the steps of separating,cleaving and detecting are performed in a continuous manner.
 29. Themethod according to claims 17 or 18 wherein the steps of separating,cleaving and detecting are performed in a continuous manner on a singledevice.
 30. The method according to claims 17 or 18 wherein the steps ofseparating, cleaving and detecting are automated.
 31. The methodaccording to claims 17 or 18 wherein said tagged molecules are generatedfrom non-3′-tagged oligonucleotide primers.
 32. The method according toclaims 17 or 18 wherein said tagged molecules are generated from taggeddideoxynucleotide terminators.
 33. The method according to claims 1, 2,or 17 wherein said target molecule is obtained from a biological sample.34. A method for detecting a single selected nucleotide within a nucleicacid molecule, comprising sequentially: (a) hybridizing in at least twoseparate reactions a tagged primer and a target nucleic acid moleculeunder conditions and for a time sufficient to permit hybridization ofsaid primer to said target nucleic acid molecule, wherein each reactioncontains an enzyme which will add a nucleotide chain terminator, and, anucleotide chain terminator complementary to adenosine, cytosine,guanosine, thymidine or uracil, and wherein each reaction contains adifferent nucleotide chain terminator; (b) separating said taggedprimers by size; (c) cleaving said tag from said tagged primer; and (d)detecting said tag by non-fluorescent spectrometry or potentiometry, andtherefrom determining the presence of said selected nucleotide withinsaid nucleic acid molecule.
 35. The method according to claim 34 whereinsaid tagged primers are separated by liquid chromatography.
 36. Themethod according to claim 34 wherein said tagged primers are separatedby HPLC.
 37. The method according to claim 34 wherein said tag isdetected by mass spectrometry, infrared spectrometry, ultravioletspectrometry, or, potentiostatic amperometry.
 38. The method accordingto claim 34 wherein said enzyme is a polymerase.
 39. The methodaccording to claim 34 wherein said target nucleic acid molecule isgenomic DNA.
 40. The method according to claim 34 wherein each reactionhas a different tag on said primer.